0s autopkgtest [15:15:57]: starting date and time: 2025-03-15 15:15:57+0000 0s autopkgtest [15:15:57]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:15:57]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.et0y7885/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade physamp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [15:16:17]: testbed dpkg architecture: armhf 22s autopkgtest [15:16:19]: testbed apt version: 2.9.33 27s autopkgtest [15:16:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 29s autopkgtest [15:16:26]: testbed release detected to be: None 36s autopkgtest [15:16:33]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 39s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 39s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 40s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 40s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 41s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 51s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 52s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 52s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 52s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 52s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 56s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 58s Fetched 41.0 MB in 20s (2103 kB/s) 59s Reading package lists... 65s autopkgtest [15:17:02]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 68s Starting 2 pkgProblemResolver with broken count: 0 68s Done 69s Entering ResolveByKeep 69s 69s Calculating upgrade... 70s The following packages will be upgraded: 70s libc-bin libc6 locales python3-jinja2 sos strace 70s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 8642 kB of archives. 70s After this operation, 23.6 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 72s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 77s Preconfiguring packages ... 78s Fetched 8642 kB in 7s (1208 kB/s) 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 78s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 78s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 78s Setting up libc6:armhf (2.41-1ubuntu2) ... 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 78s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 78s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 78s Setting up libc-bin (2.41-1ubuntu2) ... 79s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 79s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 79s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 79s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 79s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 79s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 79s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 79s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 79s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 79s Setting up sos (4.9.0-5) ... 80s Setting up locales (2.41-1ubuntu2) ... 81s Generating locales (this might take a while)... 83s en_US.UTF-8... done 83s Generation complete. 83s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 83s Setting up strace (6.13+ds-1ubuntu1) ... 83s Processing triggers for man-db (2.13.0-1) ... 84s Processing triggers for systemd (257.3-1ubuntu3) ... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 90s Solving dependencies... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [15:17:29]: rebooting testbed after setup commands that affected boot 135s autopkgtest [15:18:12]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 162s autopkgtest [15:18:39]: @@@@@@@@@@@@@@@@@@@@ apt-source physamp 172s Get:1 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (dsc) [2001 B] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (tar) [242 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky/universe physamp 1.1.0-5 (diff) [3924 B] 172s gpgv: Signature made Mon Mar 25 18:00:09 2024 UTC 172s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 172s gpgv: Can't check signature: No public key 172s dpkg-source: warning: cannot verify inline signature for ./physamp_1.1.0-5.dsc: no acceptable signature found 172s autopkgtest [15:18:49]: testing package physamp version 1.1.0-5 175s autopkgtest [15:18:52]: build not needed 177s autopkgtest [15:18:54]: test run-unit-test: preparing testbed 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s The following NEW packages will be installed: 181s libbpp-core4t64 libbpp-phyl12t64 libbpp-seq12t64 physamp 181s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 2947 kB of archives. 181s After this operation, 10.7 MB of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libbpp-core4t64 armhf 2.4.1-13 [589 kB] 182s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libbpp-seq12t64 armhf 2.4.1-13 [503 kB] 182s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libbpp-phyl12t64 armhf 2.4.1-9.1ubuntu3 [1669 kB] 182s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf physamp armhf 1.1.0-5 [186 kB] 183s Fetched 2947 kB in 1s (2457 kB/s) 183s Selecting previously unselected package libbpp-core4t64:armhf. 183s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 64655 files and directories currently installed.) 183s Preparing to unpack .../libbpp-core4t64_2.4.1-13_armhf.deb ... 183s Unpacking libbpp-core4t64:armhf (2.4.1-13) ... 183s Selecting previously unselected package libbpp-seq12t64:armhf. 183s Preparing to unpack .../libbpp-seq12t64_2.4.1-13_armhf.deb ... 183s Unpacking libbpp-seq12t64:armhf (2.4.1-13) ... 183s Selecting previously unselected package libbpp-phyl12t64:armhf. 183s Preparing to unpack .../libbpp-phyl12t64_2.4.1-9.1ubuntu3_armhf.deb ... 183s Unpacking libbpp-phyl12t64:armhf (2.4.1-9.1ubuntu3) ... 183s Selecting previously unselected package physamp. 183s Preparing to unpack .../physamp_1.1.0-5_armhf.deb ... 183s Unpacking physamp (1.1.0-5) ... 183s Setting up libbpp-core4t64:armhf (2.4.1-13) ... 183s Setting up libbpp-seq12t64:armhf (2.4.1-13) ... 183s Setting up libbpp-phyl12t64:armhf (2.4.1-9.1ubuntu3) ... 183s Setting up physamp (1.1.0-5) ... 183s Processing triggers for man-db (2.13.0-1) ... 183s Processing triggers for install-info (7.1.1-1) ... 183s Processing triggers for libc-bin (2.41-1ubuntu2) ... 193s autopkgtest [15:19:10]: test run-unit-test: [----------------------- 195s ****************************************************************** 195s * Bio++ Alignment Optimizer, version 1.1.0. * 195s * Author: J. Dutheil Last Modif. 14/03/18 * 195s * E. Figuet * 195s ****************************************************************** 195s 195s Parsing options: 195s Parsing file AlnOptimFasttree.bpp for options. 195s Alphabet type .........................: Proteic 195s Sequence file .........................: PF01049_full.txt 195s Sequence format .......................: FASTA file 195s Minimum amount of data per site........: 0.7 195s Filter gap characters..................: yes 195s Filter unresolved characters...........: yes 195s Number of reference sequences..........: 0 195s Total number of sequences..............: 1652 195s Total number of sites..................: 656 195s Input tree file .......................: PF01049_fasttree.dnd 195s Input tree format .....................: Newick 195s Comparison criterion:..................: MaxSites 195s Number of sequences in alignment.......: 1652 195s Number of sites in alignment...........: 129 195s Number of chars in alignment...........: 182603 195s Mean site entropy in alignment.........: 0.394104 195s Choice Node #seq %seq #sites %sites #chars %chars 195s 1) 2030 1647 -5 131 +2 184714 2111 195s Number of sequences in alignment.......: 1647 195s Number of sites in alignment...........: 131 195s Number of chars in alignment...........: 184714 195s Mean site entropy in alignment.........: 0.394129 195s Choice Node #seq %seq #sites %sites #chars %chars 195s 1) 1930 1645 -2 132 +1 185794 1080 196s Number of sequences in alignment.......: 1645 196s Number of sites in alignment...........: 132 196s Number of chars in alignment...........: 185794 196s Mean site entropy in alignment.........: 0.394195 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1882 1644 -1 133 +1 186920 1126 196s Number of sequences in alignment.......: 1644 196s Number of sites in alignment...........: 133 196s Number of chars in alignment...........: 186920 196s Mean site entropy in alignment.........: 0.394263 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 386 1634 -10 134 +1 187634 714 196s Number of sequences in alignment.......: 1634 196s Number of sites in alignment...........: 134 196s Number of chars in alignment...........: 187634 196s Mean site entropy in alignment.........: 0.394887 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 357 1627 -7 135 +1 188437 803 196s Number of sequences in alignment.......: 1627 196s Number of sites in alignment...........: 135 196s Number of chars in alignment...........: 188437 196s Mean site entropy in alignment.........: 0.394741 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1736 1614 -13 136 +1 188713 276 196s Number of sequences in alignment.......: 1614 196s Number of sites in alignment...........: 136 196s Number of chars in alignment...........: 188713 196s Mean site entropy in alignment.........: 0.394145 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1489 1527 -87 137 +1 181488 -7225 196s Number of sequences in alignment.......: 1527 196s Number of sites in alignment...........: 137 196s Number of chars in alignment...........: 181488 196s Mean site entropy in alignment.........: 0.378687 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 2247 1524 -3 138 +1 182435 947 196s Number of sequences in alignment.......: 1524 196s Number of sites in alignment...........: 138 196s Number of chars in alignment...........: 182435 196s Mean site entropy in alignment.........: 0.378731 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 408 1515 -9 139 +1 183008 573 196s Number of sequences in alignment.......: 1515 196s Number of sites in alignment...........: 139 196s Number of chars in alignment...........: 183008 196s Mean site entropy in alignment.........: 0.377294 196s Choice Node #seq %seq #sites %sites #chars %chars 196s 1) 1819 1488 -27 140 +1 182208 -800 197s Number of sequences in alignment.......: 1488 197s Number of sites in alignment...........: 140 197s Number of chars in alignment...........: 182208 197s Mean site entropy in alignment.........: 0.374188 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1676 1464 -24 141 +1 180695 -1513 197s Number of sequences in alignment.......: 1464 197s Number of sites in alignment...........: 141 197s Number of chars in alignment...........: 180695 197s Mean site entropy in alignment.........: 0.371696 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 416 1457 -7 142 +1 181323 628 197s Number of sequences in alignment.......: 1457 197s Number of sites in alignment...........: 142 197s Number of chars in alignment...........: 181323 197s Mean site entropy in alignment.........: 0.36917 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 1823 1371 -86 143 +1 176415 -4908 197s Number of sequences in alignment.......: 1371 197s Number of sites in alignment...........: 143 197s Number of chars in alignment...........: 176415 197s Mean site entropy in alignment.........: 0.359961 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 783 1355 -16 144 +1 175237 -1178 197s Number of sequences in alignment.......: 1355 197s Number of sites in alignment...........: 144 197s Number of chars in alignment...........: 175237 197s Mean site entropy in alignment.........: 0.360644 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 953 1307 -48 145 +1 169472 -5765 197s Number of sequences in alignment.......: 1307 197s Number of sites in alignment...........: 145 197s Number of chars in alignment...........: 169472 197s Mean site entropy in alignment.........: 0.363152 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2269 476 -831 146 +1 66187 -103285 197s Number of sequences in alignment.......: 476 197s Number of sites in alignment...........: 146 197s Number of chars in alignment...........: 66187 197s Mean site entropy in alignment.........: 0.249565 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2488 413 -63 147 +1 57456 -8731 197s Number of sequences in alignment.......: 413 197s Number of sites in alignment...........: 147 197s Number of chars in alignment...........: 57456 197s Mean site entropy in alignment.........: 0.249617 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2372 411 -2 148 +1 57619 163 197s Number of sequences in alignment.......: 411 197s Number of sites in alignment...........: 148 197s Number of chars in alignment...........: 57619 197s Mean site entropy in alignment.........: 0.248169 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 179 391 -20 149 +1 55008 -2611 197s Number of sequences in alignment.......: 391 197s Number of sites in alignment...........: 149 197s Number of chars in alignment...........: 55008 197s Mean site entropy in alignment.........: 0.249151 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2697 54 -337 151 +2 7794 -47214 197s Number of sequences in alignment.......: 54 197s Number of sites in alignment...........: 151 197s Number of chars in alignment...........: 7794 197s Mean site entropy in alignment.........: 0.0871024 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2628 50 -4 152 +1 7230 -564 197s Number of sequences in alignment.......: 50 197s Number of sites in alignment...........: 152 197s Number of chars in alignment...........: 7230 197s Mean site entropy in alignment.........: 0.0864589 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2692 48 -2 153 +1 7110 -120 197s Number of sequences in alignment.......: 48 197s Number of sites in alignment...........: 153 197s Number of chars in alignment...........: 7110 197s Mean site entropy in alignment.........: 0.0765764 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2695 10 -38 154 +1 1526 -5584 197s Number of sequences in alignment.......: 10 197s Number of sites in alignment...........: 154 197s Number of chars in alignment...........: 1526 197s Mean site entropy in alignment.........: 0.0596881 197s Choice Node #seq %seq #sites %sites #chars %chars 197s 1) 2611 2 -8 156 +2 312 -1214 197s Number of sequences in alignment.......: 2 197s Number of sites in alignment...........: 156 197s Number of chars in alignment...........: 312 197s Mean site entropy in alignment.........: 0.0190193 197s Choice Node #seq %seq #sites %sites #chars %chars 197s BppAlnOpt's done. Bye. 197s Total execution time: 0.000000d, 0.000000h, 0.000000m, 2.000000s. 197s ****************************************************************** 197s * Bio++ Alignment Optimizer, version 1.1.0. * 197s * Author: J. Dutheil Last Modif. 14/03/18 * 197s * E. Figuet * 197s ****************************************************************** 197s 197s Parsing options: 197s Parsing file AlnOptimAuto.bpp for options. 197s Alphabet type .........................: Proteic 197s Sequence file .........................: PF01049_full.txt 197s Sequence format .......................: FASTA file 197s Minimum amount of data per site........: 0.7 197s Filter gap characters..................: yes 197s Filter unresolved characters...........: yes 197s Number of reference sequences..........: 0 197s Total number of sequences..............: 1652 197s Total number of sites..................: 656 197s Compressing sequences..................: 198s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 198s Memory required to store distances (Mb): 20 198s Computing pairwise overlap matrix......: 200s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 200s Clustering linkage mode................: complete 200s Computing cluster tree.................: 206s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 206s Comparison criterion:..................: MaxSites 206s Number of sequences in alignment.......: 1652 206s Number of sites in alignment...........: 129 206s Number of chars in alignment...........: 182603 206s Mean site entropy in alignment.........: 0.394104 206s Choice Node #seq %seq #sites %sites #chars %chars 206s 1) 3294 1647 -5 131 +2 184716 2113 207s Number of sequences in alignment.......: 1647 207s Number of sites in alignment...........: 131 207s Number of chars in alignment...........: 184716 207s Mean site entropy in alignment.........: 0.394659 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3286 1645 -2 132 +1 185817 1101 207s Number of sequences in alignment.......: 1645 207s Number of sites in alignment...........: 132 207s Number of chars in alignment...........: 185817 207s Mean site entropy in alignment.........: 0.394872 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 536 1644 -1 133 +1 186943 1126 207s Number of sequences in alignment.......: 1644 207s Number of sites in alignment...........: 133 207s Number of chars in alignment...........: 186943 207s Mean site entropy in alignment.........: 0.39494 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3270 1634 -10 134 +1 187657 714 207s Number of sequences in alignment.......: 1634 207s Number of sites in alignment...........: 134 207s Number of chars in alignment...........: 187657 207s Mean site entropy in alignment.........: 0.395564 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 2951 1627 -7 135 +1 188449 792 207s Number of sequences in alignment.......: 1627 207s Number of sites in alignment...........: 135 207s Number of chars in alignment...........: 188449 207s Mean site entropy in alignment.........: 0.392385 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3021 1614 -13 136 +1 188658 209 207s Number of sequences in alignment.......: 1614 207s Number of sites in alignment...........: 136 207s Number of chars in alignment...........: 188658 207s Mean site entropy in alignment.........: 0.391197 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3235 1545 -69 137 +1 185332 -3326 207s Number of sequences in alignment.......: 1545 207s Number of sites in alignment...........: 137 207s Number of chars in alignment...........: 185332 207s Mean site entropy in alignment.........: 0.389695 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3249 1542 -3 138 +1 186300 968 207s Number of sequences in alignment.......: 1542 207s Number of sites in alignment...........: 138 207s Number of chars in alignment...........: 186300 207s Mean site entropy in alignment.........: 0.389735 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 3247 1537 -5 139 +1 187136 836 207s Number of sequences in alignment.......: 1537 207s Number of sites in alignment...........: 139 207s Number of chars in alignment...........: 187136 207s Mean site entropy in alignment.........: 0.389763 207s Choice Node #seq %seq #sites %sites #chars %chars 207s 1) 2816 1521 -16 140 +1 186509 -627 208s Number of sequences in alignment.......: 1521 208s Number of sites in alignment...........: 140 208s Number of chars in alignment...........: 186509 208s Mean site entropy in alignment.........: 0.38832 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3130 1471 -50 141 +1 183898 -2611 208s Number of sequences in alignment.......: 1471 208s Number of sites in alignment...........: 141 208s Number of chars in alignment...........: 183898 208s Mean site entropy in alignment.........: 0.370103 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 1147 1470 -1 142 +1 184902 1004 208s Number of sequences in alignment.......: 1470 208s Number of sites in alignment...........: 142 208s Number of chars in alignment...........: 184902 208s Mean site entropy in alignment.........: 0.370154 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3251 1465 -5 143 +1 185674 772 208s Number of sequences in alignment.......: 1465 208s Number of sites in alignment...........: 143 208s Number of chars in alignment...........: 185674 208s Mean site entropy in alignment.........: 0.370155 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3280 1391 -74 144 +1 181655 -4019 208s Number of sequences in alignment.......: 1391 208s Number of sites in alignment...........: 144 208s Number of chars in alignment...........: 181655 208s Mean site entropy in alignment.........: 0.359169 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 2928 1340 -51 145 +1 177148 -4507 208s Number of sequences in alignment.......: 1340 208s Number of sites in alignment...........: 145 208s Number of chars in alignment...........: 177148 208s Mean site entropy in alignment.........: 0.351822 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 3168 1159 -181 146 +1 163916 -13232 208s Number of sequences in alignment.......: 1159 208s Number of sites in alignment...........: 146 208s Number of chars in alignment...........: 163916 208s Mean site entropy in alignment.........: 0.32945 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 2651 1117 -42 147 +1 158726 -5190 208s Number of sequences in alignment.......: 1117 208s Number of sites in alignment...........: 147 208s Number of chars in alignment...........: 158726 208s Mean site entropy in alignment.........: 0.331341 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 2242 1097 -20 148 +1 156673 -2053 208s Number of sequences in alignment.......: 1097 208s Number of sites in alignment...........: 148 208s Number of chars in alignment...........: 156673 208s Mean site entropy in alignment.........: 0.324708 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 2221 1078 -19 149 +1 154673 -2000 208s Number of sequences in alignment.......: 1078 208s Number of sites in alignment...........: 149 208s Number of chars in alignment...........: 154673 208s Mean site entropy in alignment.........: 0.326137 208s Choice Node #seq %seq #sites %sites #chars %chars 208s 1) 2944 993 -85 150 +1 144901 -9772 209s Number of sequences in alignment.......: 993 209s Number of sites in alignment...........: 150 209s Number of chars in alignment...........: 144901 209s Mean site entropy in alignment.........: 0.302006 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 2554 941 -52 151 +1 137854 -7047 209s Number of sequences in alignment.......: 941 209s Number of sites in alignment...........: 151 209s Number of chars in alignment...........: 137854 209s Mean site entropy in alignment.........: 0.304205 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 2675 234 -707 157 +6 36220 -101634 209s Number of sequences in alignment.......: 234 209s Number of sites in alignment...........: 157 209s Number of chars in alignment...........: 36220 209s Mean site entropy in alignment.........: 0.18992 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 2046 230 -4 158 +1 35777 -443 209s Number of sequences in alignment.......: 230 209s Number of sites in alignment...........: 158 209s Number of chars in alignment...........: 35777 209s Mean site entropy in alignment.........: 0.188188 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1950 24 -206 160 +2 3795 -31982 209s Number of sequences in alignment.......: 24 209s Number of sites in alignment...........: 160 209s Number of chars in alignment...........: 3795 209s Mean site entropy in alignment.........: 0.185344 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1896 20 -4 161 +1 3193 -602 209s Number of sequences in alignment.......: 20 209s Number of sites in alignment...........: 161 209s Number of chars in alignment...........: 3193 209s Mean site entropy in alignment.........: 0.133241 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1795 18 -2 163 +2 2911 -282 209s Number of sequences in alignment.......: 18 209s Number of sites in alignment...........: 163 209s Number of chars in alignment...........: 2911 209s Mean site entropy in alignment.........: 0.122561 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1718 14 -4 165 +2 2294 -617 209s Number of sequences in alignment.......: 14 209s Number of sites in alignment...........: 165 209s Number of chars in alignment...........: 2294 209s Mean site entropy in alignment.........: 0.0452968 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1707 12 -2 166 +1 1983 -311 209s Number of sequences in alignment.......: 12 209s Number of sites in alignment...........: 166 209s Number of chars in alignment...........: 1983 209s Mean site entropy in alignment.........: 0.0379699 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 397 11 -1 168 +2 1838 -145 209s Number of sequences in alignment.......: 11 209s Number of sites in alignment...........: 168 209s Number of chars in alignment...........: 1838 209s Mean site entropy in alignment.........: 0.03305 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1682 8 -3 169 +1 1349 -489 209s Number of sequences in alignment.......: 8 209s Number of sites in alignment...........: 169 209s Number of chars in alignment...........: 1349 209s Mean site entropy in alignment.........: 0.0183685 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 46 7 -1 172 +3 1196 -153 209s Number of sequences in alignment.......: 7 209s Number of sites in alignment...........: 172 209s Number of chars in alignment...........: 1196 209s Mean site entropy in alignment.........: 0.0178367 209s Choice Node #seq %seq #sites %sites #chars %chars 209s 1) 1664 2 -5 176 +4 352 -844 209s Number of sequences in alignment.......: 2 209s Number of sites in alignment...........: 176 209s Number of chars in alignment...........: 352 209s Mean site entropy in alignment.........: 0.010038 209s Choice Node #seq %seq #sites %sites #chars %chars 209s BppAlnOpt's done. Bye. 209s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 209s ****************************************************************** 209s * Bio++ Alignment Optimizer, version 1.1.0. * 209s * Author: J. Dutheil Last Modif. 14/03/18 * 209s * E. Figuet * 209s ****************************************************************** 209s 209s Parsing options: 209s Parsing file AlnOptimAuto.bpp for options. 209s Alphabet type .........................: Proteic 209s Sequence file .........................: PF01049_full.txt 209s Sequence format .......................: FASTA file 209s Minimum amount of data per site........: 0.7 209s Filter gap characters..................: yes 209s Filter unresolved characters...........: yes 209s Number of reference sequences..........: 0 209s Total number of sequences..............: 1652 209s Total number of sites..................: 656 209s Compressing sequences..................: 209s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 209s Memory required to store distances (Mb): 20 209s Computing pairwise overlap matrix......: 212s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 212s Clustering linkage mode................: single 212s Computing cluster tree.................: 218s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 218s Comparison criterion:..................: MaxSites 218s Number of sequences in alignment.......: 1652 218s Number of sites in alignment...........: 129 218s Number of chars in alignment...........: 182603 218s Mean site entropy in alignment.........: 0.394104 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3297 1647 -5 131 +2 184776 2173 218s Number of sequences in alignment.......: 1647 218s Number of sites in alignment...........: 131 218s Number of chars in alignment...........: 184776 218s Mean site entropy in alignment.........: 0.394536 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3295 1645 -2 132 +1 185874 1098 218s Number of sequences in alignment.......: 1645 218s Number of sites in alignment...........: 132 218s Number of chars in alignment...........: 185874 218s Mean site entropy in alignment.........: 0.394721 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 181 1644 -1 133 +1 186998 1124 218s Number of sequences in alignment.......: 1644 218s Number of sites in alignment...........: 133 218s Number of chars in alignment...........: 186998 218s Mean site entropy in alignment.........: 0.394677 218s Choice Node #seq %seq #sites %sites #chars %chars 218s 1) 3285 1634 -10 134 +1 187772 774 219s Number of sequences in alignment.......: 1634 219s Number of sites in alignment...........: 134 219s Number of chars in alignment...........: 187772 219s Mean site entropy in alignment.........: 0.395614 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3278 1627 -7 135 +1 188620 848 219s Number of sequences in alignment.......: 1627 219s Number of sites in alignment...........: 135 219s Number of chars in alignment...........: 188620 219s Mean site entropy in alignment.........: 0.396053 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3265 1614 -13 136 +1 189192 572 219s Number of sequences in alignment.......: 1614 219s Number of sites in alignment...........: 136 219s Number of chars in alignment...........: 189192 219s Mean site entropy in alignment.........: 0.396866 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3157 1505 -109 137 +1 184306 -4886 219s Number of sequences in alignment.......: 1505 219s Number of sites in alignment...........: 137 219s Number of chars in alignment...........: 184306 219s Mean site entropy in alignment.........: 0.397698 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3139 1488 -17 138 +1 184277 -29 219s Number of sequences in alignment.......: 1488 219s Number of sites in alignment...........: 138 219s Number of chars in alignment...........: 184277 219s Mean site entropy in alignment.........: 0.396924 219s Choice Node #seq %seq #sites %sites #chars %chars 219s 1) 3136 1485 -3 139 +1 185134 857 220s Number of sequences in alignment.......: 1485 220s Number of sites in alignment...........: 139 220s Number of chars in alignment...........: 185134 220s Mean site entropy in alignment.........: 0.396707 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 3122 1471 -14 140 +1 185214 80 220s Number of sequences in alignment.......: 1471 220s Number of sites in alignment...........: 140 220s Number of chars in alignment...........: 185214 220s Mean site entropy in alignment.........: 0.396624 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2848 1437 -34 141 +1 183753 -1461 220s Number of sequences in alignment.......: 1437 220s Number of sites in alignment...........: 141 220s Number of chars in alignment...........: 183753 220s Mean site entropy in alignment.........: 0.379676 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 3110 1425 -12 142 +1 183898 145 220s Number of sequences in alignment.......: 1425 220s Number of sites in alignment...........: 142 220s Number of chars in alignment...........: 183898 220s Mean site entropy in alignment.........: 0.379975 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 3073 1387 -38 143 +1 182369 -1529 220s Number of sequences in alignment.......: 1387 220s Number of sites in alignment...........: 143 220s Number of chars in alignment...........: 182369 220s Mean site entropy in alignment.........: 0.376594 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2904 1380 -7 144 +1 182593 224 220s Number of sequences in alignment.......: 1380 220s Number of sites in alignment...........: 144 220s Number of chars in alignment...........: 182593 220s Mean site entropy in alignment.........: 0.375989 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2941 1206 -174 145 +1 167869 -14724 220s Number of sequences in alignment.......: 1206 220s Number of sites in alignment...........: 145 220s Number of chars in alignment...........: 167869 220s Mean site entropy in alignment.........: 0.346494 220s Choice Node #seq %seq #sites %sites #chars %chars 220s 1) 2829 1145 -61 146 +1 162413 -5456 221s Number of sequences in alignment.......: 1145 221s Number of sites in alignment...........: 146 221s Number of chars in alignment...........: 162413 221s Mean site entropy in alignment.........: 0.332586 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2751 1071 -74 147 +1 153723 -8690 221s Number of sequences in alignment.......: 1071 221s Number of sites in alignment...........: 147 221s Number of chars in alignment...........: 153723 221s Mean site entropy in alignment.........: 0.320762 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1751 998 -73 148 +1 144121 -9602 221s Number of sequences in alignment.......: 998 221s Number of sites in alignment...........: 148 221s Number of chars in alignment...........: 144121 221s Mean site entropy in alignment.........: 0.298818 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2100 985 -13 149 +1 142964 -1157 221s Number of sequences in alignment.......: 985 221s Number of sites in alignment...........: 149 221s Number of chars in alignment...........: 142964 221s Mean site entropy in alignment.........: 0.298279 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2427 665 -320 150 +1 97526 -45438 221s Number of sequences in alignment.......: 665 221s Number of sites in alignment...........: 150 221s Number of chars in alignment...........: 97526 221s Mean site entropy in alignment.........: 0.293825 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1379 664 -1 151 +1 97882 356 221s Number of sequences in alignment.......: 664 221s Number of sites in alignment...........: 151 221s Number of chars in alignment...........: 97882 221s Mean site entropy in alignment.........: 0.292162 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2203 441 -223 152 +1 65487 -32395 221s Number of sequences in alignment.......: 441 221s Number of sites in alignment...........: 152 221s Number of chars in alignment...........: 65487 221s Mean site entropy in alignment.........: 0.29729 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2189 427 -14 153 +1 63726 -1761 221s Number of sequences in alignment.......: 427 221s Number of sites in alignment...........: 153 221s Number of chars in alignment...........: 63726 221s Mean site entropy in alignment.........: 0.295662 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2082 334 -93 154 +1 50320 -13406 221s Number of sequences in alignment.......: 334 221s Number of sites in alignment...........: 154 221s Number of chars in alignment...........: 50320 221s Mean site entropy in alignment.........: 0.268583 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 2006 258 -76 155 +1 39190 -11130 221s Number of sequences in alignment.......: 258 221s Number of sites in alignment...........: 155 221s Number of chars in alignment...........: 39190 221s Mean site entropy in alignment.........: 0.230649 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1987 254 -4 156 +1 38780 -410 221s Number of sequences in alignment.......: 254 221s Number of sites in alignment...........: 156 221s Number of chars in alignment...........: 38780 221s Mean site entropy in alignment.........: 0.228398 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1915 247 -7 157 +1 37896 -884 221s Number of sequences in alignment.......: 247 221s Number of sites in alignment...........: 157 221s Number of chars in alignment...........: 37896 221s Mean site entropy in alignment.........: 0.226904 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1876 130 -117 158 +1 20276 -17620 221s Number of sequences in alignment.......: 130 221s Number of sites in alignment...........: 158 221s Number of chars in alignment...........: 20276 221s Mean site entropy in alignment.........: 0.134572 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1704 3 -127 163 +5 489 -19787 221s Number of sequences in alignment.......: 3 221s Number of sites in alignment...........: 163 221s Number of chars in alignment...........: 489 221s Mean site entropy in alignment.........: 0.065727 221s Choice Node #seq %seq #sites %sites #chars %chars 221s 1) 1474 2 -1 167 +4 334 -155 221s Number of sequences in alignment.......: 2 221s Number of sites in alignment...........: 167 221s Number of chars in alignment...........: 334 221s Mean site entropy in alignment.........: 0.0338121 221s Choice Node #seq %seq #sites %sites #chars %chars 221s BppAlnOpt's done. Bye. 221s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 221s ****************************************************************** 221s * Bio++ Alignment Optimizer, version 1.1.0. * 221s * Author: J. Dutheil Last Modif. 14/03/18 * 221s * E. Figuet * 221s ****************************************************************** 221s 221s Parsing options: 221s Parsing file AlnOptimAuto.bpp for options. 221s Alphabet type .........................: Proteic 221s Sequence file .........................: PF01049_full.txt 221s Sequence format .......................: FASTA file 221s Minimum amount of data per site........: 0.7 221s Filter gap characters..................: yes 221s Filter unresolved characters...........: yes 221s Number of reference sequences..........: 0 221s Total number of sequences..............: 1652 221s Total number of sites..................: 656 221s Compressing sequences..................: 221s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 221s Memory required to store distances (Mb): 20 221s Computing pairwise overlap matrix......: 224s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 224s Clustering linkage mode................: average 224s Computing cluster tree.................: 230s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 230s Comparison criterion:..................: MaxSites 230s Number of sequences in alignment.......: 1652 230s Number of sites in alignment...........: 129 230s Number of chars in alignment...........: 182603 230s Mean site entropy in alignment.........: 0.394104 230s Choice Node #seq %seq #sites %sites #chars %chars 230s 1) 3299 1647 -5 131 +2 184774 2171 231s Number of sequences in alignment.......: 1647 231s Number of sites in alignment...........: 131 231s Number of chars in alignment...........: 184774 231s Mean site entropy in alignment.........: 0.394431 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 3293 1645 -2 132 +1 185875 1101 231s Number of sequences in alignment.......: 1645 231s Number of sites in alignment...........: 132 231s Number of chars in alignment...........: 185875 231s Mean site entropy in alignment.........: 0.394643 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 181 1644 -1 133 +1 186999 1124 231s Number of sequences in alignment.......: 1644 231s Number of sites in alignment...........: 133 231s Number of chars in alignment...........: 186999 231s Mean site entropy in alignment.........: 0.394599 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 3287 1634 -10 134 +1 187779 780 231s Number of sequences in alignment.......: 1634 231s Number of sites in alignment...........: 134 231s Number of chars in alignment...........: 187779 231s Mean site entropy in alignment.........: 0.395631 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 3276 1627 -7 135 +1 188617 838 231s Number of sequences in alignment.......: 1627 231s Number of sites in alignment...........: 135 231s Number of chars in alignment...........: 188617 231s Mean site entropy in alignment.........: 0.396076 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 3238 1614 -13 136 +1 189013 396 231s Number of sequences in alignment.......: 1614 231s Number of sites in alignment...........: 136 231s Number of chars in alignment...........: 189013 231s Mean site entropy in alignment.........: 0.395128 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 3023 1533 -81 138 +2 185240 -3773 231s Number of sequences in alignment.......: 1533 231s Number of sites in alignment...........: 138 231s Number of chars in alignment...........: 185240 231s Mean site entropy in alignment.........: 0.372196 231s Choice Node #seq %seq #sites %sites #chars %chars 231s 1) 516 1532 -1 139 +1 186276 1036 232s Number of sequences in alignment.......: 1532 232s Number of sites in alignment...........: 139 232s Number of chars in alignment...........: 186276 232s Mean site entropy in alignment.........: 0.372193 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 3282 1521 -11 140 +1 186867 591 232s Number of sequences in alignment.......: 1521 232s Number of sites in alignment...........: 140 232s Number of chars in alignment...........: 186867 232s Mean site entropy in alignment.........: 0.372497 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 3105 1482 -39 141 +1 185210 -1657 232s Number of sequences in alignment.......: 1482 232s Number of sites in alignment...........: 141 232s Number of chars in alignment...........: 185210 232s Mean site entropy in alignment.........: 0.368185 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 3135 1471 -11 142 +1 185562 352 232s Number of sequences in alignment.......: 1471 232s Number of sites in alignment...........: 142 232s Number of chars in alignment...........: 185562 232s Mean site entropy in alignment.........: 0.367384 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 2863 1455 -16 143 +1 184869 -693 232s Number of sequences in alignment.......: 1455 232s Number of sites in alignment...........: 143 232s Number of chars in alignment...........: 184869 232s Mean site entropy in alignment.........: 0.366056 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 3166 1413 -42 144 +1 183102 -1767 232s Number of sequences in alignment.......: 1413 232s Number of sites in alignment...........: 144 232s Number of chars in alignment...........: 183102 232s Mean site entropy in alignment.........: 0.362023 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 2996 1204 -209 145 +1 168239 -14863 232s Number of sequences in alignment.......: 1204 232s Number of sites in alignment...........: 145 232s Number of chars in alignment...........: 168239 232s Mean site entropy in alignment.........: 0.339856 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 2960 1154 -50 146 +1 163602 -4637 232s Number of sequences in alignment.......: 1154 232s Number of sites in alignment...........: 146 232s Number of chars in alignment...........: 163602 232s Mean site entropy in alignment.........: 0.330406 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 2808 1094 -60 147 +1 157058 -6544 232s Number of sequences in alignment.......: 1094 232s Number of sites in alignment...........: 147 232s Number of chars in alignment...........: 157058 232s Mean site entropy in alignment.........: 0.314388 232s Choice Node #seq %seq #sites %sites #chars %chars 232s 1) 2635 1059 -35 148 +1 152818 -4240 233s Number of sequences in alignment.......: 1059 233s Number of sites in alignment...........: 148 233s Number of chars in alignment...........: 152818 233s Mean site entropy in alignment.........: 0.315749 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1934 1048 -11 149 +1 152007 -811 233s Number of sequences in alignment.......: 1048 233s Number of sites in alignment...........: 149 233s Number of chars in alignment...........: 152007 233s Mean site entropy in alignment.........: 0.310007 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1961 1030 -18 150 +1 150229 -1778 233s Number of sequences in alignment.......: 1030 233s Number of sites in alignment...........: 150 233s Number of chars in alignment...........: 150229 233s Mean site entropy in alignment.........: 0.303664 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2640 451 -579 151 +1 67067 -83162 233s Number of sequences in alignment.......: 451 233s Number of sites in alignment...........: 151 233s Number of chars in alignment...........: 67067 233s Mean site entropy in alignment.........: 0.278258 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2434 425 -26 152 +1 63569 -3498 233s Number of sequences in alignment.......: 425 233s Number of sites in alignment...........: 152 233s Number of chars in alignment...........: 63569 233s Mean site entropy in alignment.........: 0.276822 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2332 391 -34 153 +1 58841 -4728 233s Number of sequences in alignment.......: 391 233s Number of sites in alignment...........: 153 233s Number of chars in alignment...........: 58841 233s Mean site entropy in alignment.........: 0.269678 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2039 342 -49 154 +1 51693 -7148 233s Number of sequences in alignment.......: 342 233s Number of sites in alignment...........: 154 233s Number of chars in alignment...........: 51693 233s Mean site entropy in alignment.........: 0.250803 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2337 280 -62 155 +1 42698 -8995 233s Number of sequences in alignment.......: 280 233s Number of sites in alignment...........: 155 233s Number of chars in alignment...........: 42698 233s Mean site entropy in alignment.........: 0.230831 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1969 277 -3 156 +1 42454 -244 233s Number of sequences in alignment.......: 277 233s Number of sites in alignment...........: 156 233s Number of chars in alignment...........: 42454 233s Mean site entropy in alignment.........: 0.228862 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 2097 246 -31 157 +1 37949 -4505 233s Number of sequences in alignment.......: 246 233s Number of sites in alignment...........: 157 233s Number of chars in alignment...........: 37949 233s Mean site entropy in alignment.........: 0.216654 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 884 245 -1 158 +1 37976 27 233s Number of sequences in alignment.......: 245 233s Number of sites in alignment...........: 158 233s Number of chars in alignment...........: 37976 233s Mean site entropy in alignment.........: 0.215946 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1937 19 -226 163 +5 3067 -34909 233s Number of sequences in alignment.......: 19 233s Number of sites in alignment...........: 163 233s Number of chars in alignment...........: 3067 233s Mean site entropy in alignment.........: 0.115126 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1719 14 -5 165 +2 2297 -770 233s Number of sequences in alignment.......: 14 233s Number of sites in alignment...........: 165 233s Number of chars in alignment...........: 2297 233s Mean site entropy in alignment.........: 0.0991142 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1699 12 -2 166 +1 1983 -314 233s Number of sequences in alignment.......: 12 233s Number of sites in alignment...........: 166 233s Number of chars in alignment...........: 1983 233s Mean site entropy in alignment.........: 0.0379699 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 397 11 -1 168 +2 1838 -145 233s Number of sequences in alignment.......: 11 233s Number of sites in alignment...........: 168 233s Number of chars in alignment...........: 1838 233s Mean site entropy in alignment.........: 0.03305 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1684 8 -3 169 +1 1349 -489 233s Number of sequences in alignment.......: 8 233s Number of sites in alignment...........: 169 233s Number of chars in alignment...........: 1349 233s Mean site entropy in alignment.........: 0.0183685 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 46 7 -1 172 +3 1196 -153 233s Number of sequences in alignment.......: 7 233s Number of sites in alignment...........: 172 233s Number of chars in alignment...........: 1196 233s Mean site entropy in alignment.........: 0.0178367 233s Choice Node #seq %seq #sites %sites #chars %chars 233s 1) 1664 2 -5 176 +4 352 -844 233s Number of sequences in alignment.......: 2 233s Number of sites in alignment...........: 176 233s Number of chars in alignment...........: 352 233s Mean site entropy in alignment.........: 0.010038 233s Choice Node #seq %seq #sites %sites #chars %chars 233s BppAlnOpt's done. Bye. 233s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 233s ****************************************************************** 233s * Bio++ Alignment Optimizer, version 1.1.0. * 233s * Author: J. Dutheil Last Modif. 14/03/18 * 233s * E. Figuet * 233s ****************************************************************** 233s 233s Parsing options: 233s Parsing file AlnOptimAuto.bpp for options. 233s Alphabet type .........................: Proteic 233s Sequence file .........................: PF01049_full.txt 233s Sequence format .......................: FASTA file 233s Minimum amount of data per site........: 0.7 233s Filter gap characters..................: yes 233s Filter unresolved characters...........: yes 233s Number of reference sequences..........: 0 233s Total number of sequences..............: 1652 233s Total number of sites..................: 656 233s Compressing sequences..................: 233s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 233s Memory required to store distances (Mb): 20 233s Computing pairwise overlap matrix......: 236s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 236s Clustering linkage mode................: median 236s Computing cluster tree.................: 242s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 242s Comparison criterion:..................: MaxSites 242s Number of sequences in alignment.......: 1652 242s Number of sites in alignment...........: 129 242s Number of chars in alignment...........: 182603 242s Mean site entropy in alignment.........: 0.394104 242s Choice Node #seq %seq #sites %sites #chars %chars 242s 1) 3297 1647 -5 131 +2 184774 2171 242s Number of sequences in alignment.......: 1647 242s Number of sites in alignment...........: 131 242s Number of chars in alignment...........: 184774 242s Mean site entropy in alignment.........: 0.394431 242s Choice Node #seq %seq #sites %sites #chars %chars 242s 1) 3295 1645 -2 132 +1 185873 1099 242s Number of sequences in alignment.......: 1645 242s Number of sites in alignment...........: 132 242s Number of chars in alignment...........: 185873 242s Mean site entropy in alignment.........: 0.394618 242s Choice Node #seq %seq #sites %sites #chars %chars 242s 1) 275 1644 -1 133 +1 186998 1125 242s Number of sequences in alignment.......: 1644 242s Number of sites in alignment...........: 133 242s Number of chars in alignment...........: 186998 242s Mean site entropy in alignment.........: 0.394724 242s Choice Node #seq %seq #sites %sites #chars %chars 242s 1) 3280 1630 -14 134 +1 187559 561 243s Number of sequences in alignment.......: 1630 243s Number of sites in alignment...........: 134 243s Number of chars in alignment...........: 187559 243s Mean site entropy in alignment.........: 0.39546 243s Choice Node #seq %seq #sites %sites #chars %chars 243s 1) 3272 1622 -8 135 +1 188376 817 244s Number of sequences in alignment.......: 1622 244s Number of sites in alignment...........: 135 244s Number of chars in alignment...........: 188376 244s Mean site entropy in alignment.........: 0.396213 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3261 1611 -11 136 +1 189031 655 244s Number of sequences in alignment.......: 1611 244s Number of sites in alignment...........: 136 244s Number of chars in alignment...........: 189031 244s Mean site entropy in alignment.........: 0.396902 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3184 1534 -77 137 +1 185562 -3469 244s Number of sequences in alignment.......: 1534 244s Number of sites in alignment...........: 137 244s Number of chars in alignment...........: 185562 244s Mean site entropy in alignment.........: 0.396433 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3182 1532 -2 138 +1 186503 941 244s Number of sequences in alignment.......: 1532 244s Number of sites in alignment...........: 138 244s Number of chars in alignment...........: 186503 244s Mean site entropy in alignment.........: 0.396422 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 513 1531 -1 139 +1 187535 1032 244s Number of sequences in alignment.......: 1531 244s Number of sites in alignment...........: 139 244s Number of chars in alignment...........: 187535 244s Mean site entropy in alignment.........: 0.396222 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3169 1518 -13 140 +1 187760 225 244s Number of sequences in alignment.......: 1518 244s Number of sites in alignment...........: 140 244s Number of chars in alignment...........: 187760 244s Mean site entropy in alignment.........: 0.395785 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3125 1475 -43 141 +1 185962 -1798 244s Number of sequences in alignment.......: 1475 244s Number of sites in alignment...........: 141 244s Number of chars in alignment...........: 185962 244s Mean site entropy in alignment.........: 0.388512 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3117 1467 -8 142 +1 186502 540 244s Number of sequences in alignment.......: 1467 244s Number of sites in alignment...........: 142 244s Number of chars in alignment...........: 186502 244s Mean site entropy in alignment.........: 0.388016 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3102 1452 -15 143 +1 186490 -12 244s Number of sequences in alignment.......: 1452 244s Number of sites in alignment...........: 143 244s Number of chars in alignment...........: 186490 244s Mean site entropy in alignment.........: 0.386609 244s Choice Node #seq %seq #sites %sites #chars %chars 244s 1) 3052 1402 -50 144 +1 183727 -2763 245s Number of sequences in alignment.......: 1402 245s Number of sites in alignment...........: 144 245s Number of chars in alignment...........: 183727 245s Mean site entropy in alignment.........: 0.379315 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2877 1227 -175 145 +1 170235 -13492 245s Number of sequences in alignment.......: 1227 245s Number of sites in alignment...........: 145 245s Number of chars in alignment...........: 170235 245s Mean site entropy in alignment.........: 0.34859 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2788 1138 -89 146 +1 161621 -8614 245s Number of sequences in alignment.......: 1138 245s Number of sites in alignment...........: 146 245s Number of chars in alignment...........: 161621 245s Mean site entropy in alignment.........: 0.330459 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2731 1081 -57 147 +1 155136 -6485 245s Number of sequences in alignment.......: 1081 245s Number of sites in alignment...........: 147 245s Number of chars in alignment...........: 155136 245s Mean site entropy in alignment.........: 0.319787 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1701 1030 -51 148 +1 148555 -6581 245s Number of sequences in alignment.......: 1030 245s Number of sites in alignment...........: 148 245s Number of chars in alignment...........: 148555 245s Mean site entropy in alignment.........: 0.305707 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2499 798 -232 149 +1 116805 -31750 245s Number of sequences in alignment.......: 798 245s Number of sites in alignment...........: 149 245s Number of chars in alignment...........: 116805 245s Mean site entropy in alignment.........: 0.273968 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2468 767 -31 150 +1 112894 -3911 245s Number of sequences in alignment.......: 767 245s Number of sites in alignment...........: 150 245s Number of chars in alignment...........: 112894 245s Mean site entropy in alignment.........: 0.272075 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2239 538 -229 151 +1 79674 -33220 245s Number of sequences in alignment.......: 538 245s Number of sites in alignment...........: 151 245s Number of chars in alignment...........: 79674 245s Mean site entropy in alignment.........: 0.280963 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2196 495 -43 152 +1 73702 -5972 245s Number of sequences in alignment.......: 495 245s Number of sites in alignment...........: 152 245s Number of chars in alignment...........: 73702 245s Mean site entropy in alignment.........: 0.28148 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2076 375 -120 153 +1 56316 -17386 245s Number of sequences in alignment.......: 375 245s Number of sites in alignment...........: 153 245s Number of chars in alignment...........: 56316 245s Mean site entropy in alignment.........: 0.267502 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 2018 317 -58 154 +1 47977 -8339 245s Number of sequences in alignment.......: 317 245s Number of sites in alignment...........: 154 245s Number of chars in alignment...........: 47977 245s Mean site entropy in alignment.........: 0.249671 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1949 248 -69 155 +1 37817 -10160 245s Number of sequences in alignment.......: 248 245s Number of sites in alignment...........: 155 245s Number of chars in alignment...........: 37817 245s Mean site entropy in alignment.........: 0.215239 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1938 237 -11 156 +1 36376 -1441 245s Number of sequences in alignment.......: 237 245s Number of sites in alignment...........: 156 245s Number of chars in alignment...........: 36376 245s Mean site entropy in alignment.........: 0.201826 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1926 225 -12 157 +1 34752 -1624 245s Number of sequences in alignment.......: 225 245s Number of sites in alignment...........: 157 245s Number of chars in alignment...........: 34752 245s Mean site entropy in alignment.........: 0.184033 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1779 78 -147 158 +1 12282 -22470 245s Number of sequences in alignment.......: 78 245s Number of sites in alignment...........: 158 245s Number of chars in alignment...........: 12282 245s Mean site entropy in alignment.........: 0.0830049 245s Choice Node #seq %seq #sites %sites #chars %chars 245s 1) 1703 2 -76 160 +2 320 -11962 245s Number of sequences in alignment.......: 2 245s Number of sites in alignment...........: 160 245s Number of chars in alignment...........: 320 245s Mean site entropy in alignment.........: 0 245s Choice Node #seq %seq #sites %sites #chars %chars 245s BppAlnOpt's done. Bye. 245s Total execution time: 0.000000d, 0.000000h, 0.000000m, 12.000000s. 245s ****************************************************************** 245s * Bio++ Alignment Optimizer, version 1.1.0. * 245s * Author: J. Dutheil Last Modif. 14/03/18 * 245s * E. Figuet * 245s ****************************************************************** 245s 245s Parsing options: 245s Parsing file AlnOptimAuto.bpp for options. 245s Alphabet type .........................: Proteic 245s Sequence file .........................: PF01049_full.txt 245s Sequence format .......................: FASTA file 245s Minimum amount of data per site........: 0.7 245s Filter gap characters..................: yes 245s Filter unresolved characters...........: yes 245s Number of reference sequences..........: 0 245s Total number of sequences..............: 1652 245s Total number of sites..................: 656 245s Compressing sequences..................: 246s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 246s Memory required to store distances (Mb): 20 246s Computing pairwise overlap matrix......: 248s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 248s Clustering linkage mode................: centroid 248s Computing cluster tree.................: 255s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 255s Comparison criterion:..................: MaxSites 255s Number of sequences in alignment.......: 1652 255s Number of sites in alignment...........: 129 255s Number of chars in alignment...........: 182603 255s Mean site entropy in alignment.........: 0.394104 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3297 1647 -5 131 +2 184783 2180 255s Number of sequences in alignment.......: 1647 255s Number of sites in alignment...........: 131 255s Number of chars in alignment...........: 184783 255s Mean site entropy in alignment.........: 0.394537 255s Choice Node #seq %seq #sites %sites #chars %chars 255s 1) 3295 1645 -2 132 +1 185880 1097 256s Number of sequences in alignment.......: 1645 256s Number of sites in alignment...........: 132 256s Number of chars in alignment...........: 185880 256s Mean site entropy in alignment.........: 0.394662 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 181 1644 -1 133 +1 187004 1124 256s Number of sequences in alignment.......: 1644 256s Number of sites in alignment...........: 133 256s Number of chars in alignment...........: 187004 256s Mean site entropy in alignment.........: 0.394618 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3284 1634 -10 134 +1 187785 781 256s Number of sequences in alignment.......: 1634 256s Number of sites in alignment...........: 134 256s Number of chars in alignment...........: 187785 256s Mean site entropy in alignment.........: 0.395449 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3277 1627 -7 135 +1 188649 864 256s Number of sequences in alignment.......: 1627 256s Number of sites in alignment...........: 135 256s Number of chars in alignment...........: 188649 256s Mean site entropy in alignment.........: 0.395884 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3264 1614 -13 136 +1 189270 621 256s Number of sequences in alignment.......: 1614 256s Number of sites in alignment...........: 136 256s Number of chars in alignment...........: 189270 256s Mean site entropy in alignment.........: 0.396209 256s Choice Node #seq %seq #sites %sites #chars %chars 256s 1) 3158 1508 -106 137 +1 184807 -4463 257s Number of sequences in alignment.......: 1508 257s Number of sites in alignment...........: 137 257s Number of chars in alignment...........: 184807 257s Mean site entropy in alignment.........: 0.391659 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 3141 1491 -17 138 +1 184810 3 257s Number of sequences in alignment.......: 1491 257s Number of sites in alignment...........: 138 257s Number of chars in alignment...........: 184810 257s Mean site entropy in alignment.........: 0.389899 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 3135 1485 -6 139 +1 185468 658 257s Number of sequences in alignment.......: 1485 257s Number of sites in alignment...........: 139 257s Number of chars in alignment...........: 185468 257s Mean site entropy in alignment.........: 0.389868 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 3124 1474 -11 140 +1 185788 320 257s Number of sequences in alignment.......: 1474 257s Number of sites in alignment...........: 140 257s Number of chars in alignment...........: 185788 257s Mean site entropy in alignment.........: 0.389071 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 3091 1441 -33 141 +1 184655 -1133 257s Number of sequences in alignment.......: 1441 257s Number of sites in alignment...........: 141 257s Number of chars in alignment...........: 184655 257s Mean site entropy in alignment.........: 0.38709 257s Choice Node #seq %seq #sites %sites #chars %chars 257s 1) 3077 1427 -14 142 +1 184714 59 258s Number of sequences in alignment.......: 1427 258s Number of sites in alignment...........: 142 258s Number of chars in alignment...........: 184714 258s Mean site entropy in alignment.........: 0.386526 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 3055 1405 -22 144 +2 185186 472 258s Number of sequences in alignment.......: 1405 258s Number of sites in alignment...........: 144 258s Number of chars in alignment...........: 185186 258s Mean site entropy in alignment.........: 0.383626 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2907 1257 -148 145 +1 173927 -11259 258s Number of sequences in alignment.......: 1257 258s Number of sites in alignment...........: 145 258s Number of chars in alignment...........: 173927 258s Mean site entropy in alignment.........: 0.350796 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2807 1157 -100 146 +1 163983 -9944 258s Number of sequences in alignment.......: 1157 258s Number of sites in alignment...........: 146 258s Number of chars in alignment...........: 163983 258s Mean site entropy in alignment.........: 0.329626 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2748 1098 -59 147 +1 157592 -6391 258s Number of sequences in alignment.......: 1098 258s Number of sites in alignment...........: 147 258s Number of chars in alignment...........: 157592 258s Mean site entropy in alignment.........: 0.314432 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 1678 1070 -28 148 +1 154399 -3193 258s Number of sequences in alignment.......: 1070 258s Number of sites in alignment...........: 148 258s Number of chars in alignment...........: 154399 258s Mean site entropy in alignment.........: 0.303382 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2620 942 -128 149 +1 137516 -16883 258s Number of sequences in alignment.......: 942 258s Number of sites in alignment...........: 149 258s Number of chars in alignment...........: 137516 258s Mean site entropy in alignment.........: 0.284952 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2615 937 -5 150 +1 137462 -54 258s Number of sequences in alignment.......: 937 258s Number of sites in alignment...........: 150 258s Number of chars in alignment...........: 137462 258s Mean site entropy in alignment.........: 0.285064 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2320 642 -295 151 +1 95140 -42322 258s Number of sequences in alignment.......: 642 258s Number of sites in alignment...........: 151 258s Number of chars in alignment...........: 95140 258s Mean site entropy in alignment.........: 0.276628 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2179 501 -141 152 +1 74734 -20406 258s Number of sequences in alignment.......: 501 258s Number of sites in alignment...........: 152 258s Number of chars in alignment...........: 74734 258s Mean site entropy in alignment.........: 0.281366 258s Choice Node #seq %seq #sites %sites #chars %chars 258s 1) 2108 430 -71 153 +1 64604 -10130 259s Number of sequences in alignment.......: 430 259s Number of sites in alignment...........: 153 259s Number of chars in alignment...........: 64604 259s Mean site entropy in alignment.........: 0.282214 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 2038 360 -70 154 +1 54522 -10082 259s Number of sequences in alignment.......: 360 259s Number of sites in alignment...........: 154 259s Number of chars in alignment...........: 54522 259s Mean site entropy in alignment.........: 0.265356 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 1969 291 -69 155 +1 44461 -10061 259s Number of sequences in alignment.......: 291 259s Number of sites in alignment...........: 155 259s Number of chars in alignment...........: 44461 259s Mean site entropy in alignment.........: 0.240018 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 1956 278 -13 156 +1 42693 -1768 259s Number of sequences in alignment.......: 278 259s Number of sites in alignment...........: 156 259s Number of chars in alignment...........: 42693 259s Mean site entropy in alignment.........: 0.236678 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 1925 247 -31 157 +1 38195 -4498 259s Number of sequences in alignment.......: 247 259s Number of sites in alignment...........: 157 259s Number of chars in alignment...........: 38195 259s Mean site entropy in alignment.........: 0.216008 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 1923 245 -2 158 +1 38065 -130 259s Number of sequences in alignment.......: 245 259s Number of sites in alignment...........: 158 259s Number of chars in alignment...........: 38065 259s Mean site entropy in alignment.........: 0.215165 259s Choice Node #seq %seq #sites %sites #chars %chars 259s 1) 610 1 -244 177 +19 177 -37888 259s Number of sequences in alignment.......: 1 259s Number of sites in alignment...........: 177 259s Number of chars in alignment...........: 177 259s Mean site entropy in alignment.........: 0 259s Choice Node #seq %seq #sites %sites #chars %chars 259s BppAlnOpt's done. Bye. 259s Total execution time: 0.000000d, 0.000000h, 0.000000m, 14.000000s. 259s ****************************************************************** 259s * Bio++ Alignment Optimizer, version 1.1.0. * 259s * Author: J. Dutheil Last Modif. 14/03/18 * 259s * E. Figuet * 259s ****************************************************************** 259s 259s Parsing options: 259s Parsing file AlnOptimAuto.bpp for options. 259s Alphabet type .........................: Proteic 259s Sequence file .........................: PF01049_full.txt 259s Sequence format .......................: FASTA file 259s Minimum amount of data per site........: 0.7 259s Filter gap characters..................: yes 259s Filter unresolved characters...........: yes 259s Number of reference sequences..........: 0 259s Total number of sequences..............: 1652 259s Total number of sites..................: 656 259s Compressing sequences..................: 259s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 259s Memory required to store distances (Mb): 20 259s Computing pairwise overlap matrix......: 261s [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 28% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 57% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 65% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 78% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 86% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 94% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 261s Clustering linkage mode................: ward 261s Computing cluster tree.................: 267s [ ] 0% [> ] 2% [>> ] 5% [>>> ] 8% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 16% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 24% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 32% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 37% [>>>>>>>>>>>>>>> ] 40% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 45% [>>>>>>>>>>>>>>>>>> ] 48% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 53% [>>>>>>>>>>>>>>>>>>>>> ] 56% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 61% [>>>>>>>>>>>>>>>>>>>>>>>> ] 64% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 69% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 74% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 77% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 82% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 88% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 90% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 96% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 98% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%Done. 268s Comparison criterion:..................: MaxSites 268s Number of sequences in alignment.......: 1652 268s Number of sites in alignment...........: 129 268s Number of chars in alignment...........: 182603 268s Mean site entropy in alignment.........: 0.394104 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 3251 1647 -5 131 +2 184716 2113 268s Number of sequences in alignment.......: 1647 268s Number of sites in alignment...........: 131 268s Number of chars in alignment...........: 184716 268s Mean site entropy in alignment.........: 0.394659 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 3239 1645 -2 132 +1 185817 1101 268s Number of sequences in alignment.......: 1645 268s Number of sites in alignment...........: 132 268s Number of chars in alignment...........: 185817 268s Mean site entropy in alignment.........: 0.394872 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 1147 1644 -1 133 +1 186943 1126 268s Number of sequences in alignment.......: 1644 268s Number of sites in alignment...........: 133 268s Number of chars in alignment...........: 186943 268s Mean site entropy in alignment.........: 0.394935 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 3219 1634 -10 134 +1 187657 714 268s Number of sequences in alignment.......: 1634 268s Number of sites in alignment...........: 134 268s Number of chars in alignment...........: 187657 268s Mean site entropy in alignment.........: 0.395559 268s Choice Node #seq %seq #sites %sites #chars %chars 268s 1) 3259 1627 -7 135 +1 188588 931 268s Number of sequences in alignment.......: 1627 269s Number of sites in alignment...........: 135 269s Number of chars in alignment...........: 188588 269s Mean site entropy in alignment.........: 0.39614 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3098 1614 -13 136 +1 188375 -213 269s Number of sequences in alignment.......: 1614 269s Number of sites in alignment...........: 136 269s Number of chars in alignment...........: 188375 269s Mean site entropy in alignment.........: 0.394599 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3276 1530 -84 139 +3 185744 -2631 269s Number of sequences in alignment.......: 1530 269s Number of sites in alignment...........: 139 269s Number of chars in alignment...........: 185744 269s Mean site entropy in alignment.........: 0.386989 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3232 1521 -9 140 +1 186359 615 269s Number of sequences in alignment.......: 1521 269s Number of sites in alignment...........: 140 269s Number of chars in alignment...........: 186359 269s Mean site entropy in alignment.........: 0.387231 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3100 1471 -50 141 +1 182091 -4268 269s Number of sequences in alignment.......: 1471 269s Number of sites in alignment...........: 141 269s Number of chars in alignment...........: 182091 269s Mean site entropy in alignment.........: 0.382183 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3094 1451 -20 142 +1 181641 -450 269s Number of sequences in alignment.......: 1451 269s Number of sites in alignment...........: 142 269s Number of chars in alignment...........: 181641 269s Mean site entropy in alignment.........: 0.377306 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3289 1405 -46 143 +1 179756 -1885 269s Number of sequences in alignment.......: 1405 269s Number of sites in alignment...........: 143 269s Number of chars in alignment...........: 179756 269s Mean site entropy in alignment.........: 0.373661 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3024 1397 -8 144 +1 180270 514 269s Number of sequences in alignment.......: 1397 269s Number of sites in alignment...........: 144 269s Number of chars in alignment...........: 180270 269s Mean site entropy in alignment.........: 0.372275 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3298 1308 -89 145 +1 175625 -4645 269s Number of sequences in alignment.......: 1308 269s Number of sites in alignment...........: 145 269s Number of chars in alignment...........: 175625 269s Mean site entropy in alignment.........: 0.348431 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3290 1161 -147 146 +1 156442 -19183 269s Number of sequences in alignment.......: 1161 269s Number of sites in alignment...........: 146 269s Number of chars in alignment...........: 156442 269s Mean site entropy in alignment.........: 0.328649 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2555 1150 -11 147 +1 155751 -691 269s Number of sequences in alignment.......: 1150 269s Number of sites in alignment...........: 147 269s Number of chars in alignment...........: 155751 269s Mean site entropy in alignment.........: 0.328421 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2516 1111 -39 148 +1 150876 -4875 269s Number of sequences in alignment.......: 1111 269s Number of sites in alignment...........: 148 269s Number of chars in alignment...........: 150876 269s Mean site entropy in alignment.........: 0.331041 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3202 1094 -17 149 +1 150055 -821 269s Number of sequences in alignment.......: 1094 269s Number of sites in alignment...........: 149 269s Number of chars in alignment...........: 150055 269s Mean site entropy in alignment.........: 0.325678 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3283 1034 -60 150 +1 144300 -5755 269s Number of sequences in alignment.......: 1034 269s Number of sites in alignment...........: 150 269s Number of chars in alignment...........: 144300 269s Mean site entropy in alignment.........: 0.310772 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3201 869 -165 151 +1 120684 -23616 269s Number of sequences in alignment.......: 869 269s Number of sites in alignment...........: 151 269s Number of chars in alignment...........: 120684 269s Mean site entropy in alignment.........: 0.320746 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 3206 867 -2 152 +1 121198 514 269s Number of sequences in alignment.......: 867 269s Number of sites in alignment...........: 152 269s Number of chars in alignment...........: 121198 269s Mean site entropy in alignment.........: 0.32085 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 2890 153 -714 157 +5 23971 -97227 269s Number of sequences in alignment.......: 153 269s Number of sites in alignment...........: 157 269s Number of chars in alignment...........: 23971 269s Mean site entropy in alignment.........: 0.0601394 269s Choice Node #seq %seq #sites %sites #chars %chars 269s 1) 1887 117 -36 158 +1 18405 -5566 269s Number of sequences in alignment.......: 117 269s Number of sites in alignment...........: 158 269s Number of chars in alignment...........: 18405 269s Mean site entropy in alignment.........: 0.0581426 269s Choice Node #seq %seq #sites %sites #chars %chars 269s BppAlnOpt's done. Bye. 269s Total execution time: 0.000000d, 0.000000h, 0.000000m, 10.000000s. 269s ****************************************************************** 269s * Bio++ Alignment Optimizer, version 1.1.0. * 269s * Author: J. Dutheil Last Modif. 14/03/18 * 269s * E. Figuet * 269s ****************************************************************** 269s 269s Parsing options: 269s Parsing file AlnOptimFasttreeStop.bpp for options. 269s Alphabet type .........................: Proteic 269s Sequence file .........................: PF01049_full.txt 269s Sequence format .......................: FASTA file 270s Minimum amount of data per site........: 0.7 270s Filter gap characters..................: yes 270s Filter unresolved characters...........: yes 270s Number of reference sequences..........: 0 270s Total number of sequences..............: 1652 270s Total number of sites..................: 656 270s Input tree file .......................: PF01049_fasttree.dnd 270s Input tree format .....................: Newick 270s Minimum number of sequences to keep....: 826 270s Comparison criterion:..................: MaxSites 270s Number of sequences in alignment.......: 1652 270s Number of sites in alignment...........: 129 270s Number of chars in alignment...........: 182603 270s Mean site entropy in alignment.........: 0.394104 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 2030 1647 -5 131 +2 184714 2111 270s Number of sequences in alignment.......: 1647 270s Number of sites in alignment...........: 131 270s Number of chars in alignment...........: 184714 270s Mean site entropy in alignment.........: 0.394129 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 1930 1645 -2 132 +1 185794 1080 270s Number of sequences in alignment.......: 1645 270s Number of sites in alignment...........: 132 270s Number of chars in alignment...........: 185794 270s Mean site entropy in alignment.........: 0.394195 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 1882 1644 -1 133 +1 186920 1126 270s Number of sequences in alignment.......: 1644 270s Number of sites in alignment...........: 133 270s Number of chars in alignment...........: 186920 270s Mean site entropy in alignment.........: 0.394263 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 386 1634 -10 134 +1 187634 714 270s Number of sequences in alignment.......: 1634 270s Number of sites in alignment...........: 134 270s Number of chars in alignment...........: 187634 270s Mean site entropy in alignment.........: 0.394887 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 357 1627 -7 135 +1 188437 803 270s Number of sequences in alignment.......: 1627 270s Number of sites in alignment...........: 135 270s Number of chars in alignment...........: 188437 270s Mean site entropy in alignment.........: 0.394741 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 1736 1614 -13 136 +1 188713 276 270s Number of sequences in alignment.......: 1614 270s Number of sites in alignment...........: 136 270s Number of chars in alignment...........: 188713 270s Mean site entropy in alignment.........: 0.394145 270s Choice Node #seq %seq #sites %sites #chars %chars 270s 1) 1489 1527 -87 137 +1 181488 -7225 271s Number of sequences in alignment.......: 1527 271s Number of sites in alignment...........: 137 271s Number of chars in alignment...........: 181488 271s Mean site entropy in alignment.........: 0.378687 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 2247 1524 -3 138 +1 182435 947 271s Number of sequences in alignment.......: 1524 271s Number of sites in alignment...........: 138 271s Number of chars in alignment...........: 182435 271s Mean site entropy in alignment.........: 0.378731 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 408 1515 -9 139 +1 183008 573 271s Number of sequences in alignment.......: 1515 271s Number of sites in alignment...........: 139 271s Number of chars in alignment...........: 183008 271s Mean site entropy in alignment.........: 0.377294 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 1819 1488 -27 140 +1 182208 -800 271s Number of sequences in alignment.......: 1488 271s Number of sites in alignment...........: 140 271s Number of chars in alignment...........: 182208 271s Mean site entropy in alignment.........: 0.374188 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 1676 1464 -24 141 +1 180695 -1513 271s Number of sequences in alignment.......: 1464 271s Number of sites in alignment...........: 141 271s Number of chars in alignment...........: 180695 271s Mean site entropy in alignment.........: 0.371696 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 416 1457 -7 142 +1 181323 628 271s Number of sequences in alignment.......: 1457 271s Number of sites in alignment...........: 142 271s Number of chars in alignment...........: 181323 271s Mean site entropy in alignment.........: 0.36917 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 1823 1371 -86 143 +1 176415 -4908 271s Number of sequences in alignment.......: 1371 271s Number of sites in alignment...........: 143 271s Number of chars in alignment...........: 176415 271s Mean site entropy in alignment.........: 0.359961 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 783 1355 -16 144 +1 175237 -1178 271s Number of sequences in alignment.......: 1355 271s Number of sites in alignment...........: 144 271s Number of chars in alignment...........: 175237 271s Mean site entropy in alignment.........: 0.360644 271s Choice Node #seq %seq #sites %sites #chars %chars 271s 1) 953 1307 -48 145 +1 169472 -5765 271s Number of sequences in alignment.......: 1307 271s Number of sites in alignment...........: 145 271s Number of chars in alignment...........: 169472 271s Mean site entropy in alignment.........: 0.363152 271s Choice Node #seq %seq #sites %sites #chars %chars 271s Output alignment file .................: PF01049_optimized_fastml.fasta 271s Output alignment format ...............: FASTA file 272s Output tree file ......................: PF01049_optimized_fastml.dnd 272s Output tree format ....................: Newick 272s BppAlnOpt's done. Bye. 272s Total execution time: 0.000000d, 0.000000h, 0.000000m, 3.000000s. 272s PASS 273s autopkgtest [15:20:30]: test run-unit-test: -----------------------] 278s run-unit-test PASS 278s autopkgtest [15:20:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 283s autopkgtest [15:20:40]: @@@@@@@@@@@@@@@@@@@@ summary 283s run-unit-test PASS