0s autopkgtest [18:07:19]: starting date and time: 2025-03-15 18:07:19+0000 0s autopkgtest [18:07:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:07:19]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.uptq_vni/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 tree-puzzle --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.210 lxd-armhf-10.145.243.210:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [18:07:39]: testbed dpkg architecture: armhf 22s autopkgtest [18:07:41]: testbed apt version: 2.9.33 26s autopkgtest [18:07:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 27s autopkgtest [18:07:46]: testbed release detected to be: None 35s autopkgtest [18:07:54]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 41s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 41s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 41s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 41s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 41s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 41s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 41s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 65s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 67s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 68s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 68s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 68s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 84s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 86s Fetched 41.0 MB in 48s (847 kB/s) 87s Reading package lists... 92s autopkgtest [18:08:51]: upgrading testbed (apt dist-upgrade and autopurge) 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 99s Entering ResolveByKeep 99s 100s Calculating upgrade... 101s The following packages will be upgraded: 101s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 101s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 8683 kB of archives. 101s After this operation, 23.6 kB of additional disk space will be used. 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 109s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 109s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 110s Preconfiguring packages ... 110s Fetched 8683 kB in 8s (1062 kB/s) 110s (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.) 110s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 111s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc6:armhf (2.41-1ubuntu2) ... 111s (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.) 111s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 111s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc-bin (2.41-1ubuntu2) ... 111s (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.) 111s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 111s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 112s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 112s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 112s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 112s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 112s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 112s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 112s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 113s Setting up sos (4.9.0-5) ... 113s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 113s Setting up locales (2.41-1ubuntu2) ... 114s Generating locales (this might take a while)... 116s en_US.UTF-8... done 116s Generation complete. 117s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 117s Setting up strace (6.13+ds-1ubuntu1) ... 117s Processing triggers for man-db (2.13.0-1) ... 118s Processing triggers for systemd (257.3-1ubuntu3) ... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 122s Starting pkgProblemResolver with broken count: 0 122s Starting 2 pkgProblemResolver with broken count: 0 122s Done 122s Solving dependencies... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s autopkgtest [18:09:24]: rebooting testbed after setup commands that affected boot 165s autopkgtest [18:10:04]: 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 202s autopkgtest [18:10:41]: @@@@@@@@@@@@@@@@@@@@ apt-source tree-puzzle 221s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (dsc) [2235 B] 221s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (tar) [591 kB] 221s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tree-puzzle 5.3~rc16+dfsg-12build1 (diff) [32.4 kB] 222s gpgv: Signature made Sat Nov 30 06:14:46 2024 UTC 222s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 222s gpgv: Can't check signature: No public key 222s dpkg-source: warning: cannot verify inline signature for ./tree-puzzle_5.3~rc16+dfsg-12build1.dsc: no acceptable signature found 222s autopkgtest [18:11:01]: testing package tree-puzzle version 5.3~rc16+dfsg-12build1 225s autopkgtest [18:11:04]: build not needed 228s autopkgtest [18:11:07]: test run-unit-test: preparing testbed 230s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s Starting pkgProblemResolver with broken count: 0 230s Starting 2 pkgProblemResolver with broken count: 0 230s Done 231s The following NEW packages will be installed: 231s hwloc-nox libgfortran5 libhwloc15 libmpich12 libslurm42t64 libsprng2 231s mpi-default-bin mpich tree-ppuzzle tree-puzzle tree-puzzle-doc 232s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 232s Need to get 4079 kB of archives. 232s After this operation, 10.9 MB of additional disk space will be used. 232s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 232s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhwloc15 armhf 2.12.0-1 [147 kB] 232s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libslurm42t64 armhf 24.11.1-1 [769 kB] 233s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libsprng2 armhf 2.0a-16 [91.6 kB] 233s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libmpich12 armhf 4.2.1-5 [1574 kB] 235s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf hwloc-nox armhf 2.12.0-1 [213 kB] 235s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf mpich armhf 4.2.1-5 [214 kB] 236s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf mpi-default-bin armhf 1.18 [2504 B] 236s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf tree-ppuzzle armhf 5.3~rc16+dfsg-12build1 [172 kB] 236s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf tree-puzzle armhf 5.3~rc16+dfsg-12build1 [155 kB] 236s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf tree-puzzle-doc all 5.3~rc16+dfsg-12build1 [409 kB] 237s Fetched 4079 kB in 5s (840 kB/s) 237s Selecting previously unselected package libgfortran5:armhf. 237s (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.) 237s Preparing to unpack .../00-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 237s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 237s Selecting previously unselected package libhwloc15:armhf. 237s Preparing to unpack .../01-libhwloc15_2.12.0-1_armhf.deb ... 237s Unpacking libhwloc15:armhf (2.12.0-1) ... 237s Selecting previously unselected package libslurm42t64. 237s Preparing to unpack .../02-libslurm42t64_24.11.1-1_armhf.deb ... 237s Unpacking libslurm42t64 (24.11.1-1) ... 237s Selecting previously unselected package libsprng2. 237s Preparing to unpack .../03-libsprng2_2.0a-16_armhf.deb ... 237s Unpacking libsprng2 (2.0a-16) ... 237s Selecting previously unselected package libmpich12:armhf. 237s Preparing to unpack .../04-libmpich12_4.2.1-5_armhf.deb ... 237s Unpacking libmpich12:armhf (4.2.1-5) ... 237s Selecting previously unselected package hwloc-nox. 237s Preparing to unpack .../05-hwloc-nox_2.12.0-1_armhf.deb ... 237s Unpacking hwloc-nox (2.12.0-1) ... 237s Selecting previously unselected package mpich. 237s Preparing to unpack .../06-mpich_4.2.1-5_armhf.deb ... 237s Unpacking mpich (4.2.1-5) ... 237s Selecting previously unselected package mpi-default-bin. 237s Preparing to unpack .../07-mpi-default-bin_1.18_armhf.deb ... 237s Unpacking mpi-default-bin (1.18) ... 237s Selecting previously unselected package tree-ppuzzle. 237s Preparing to unpack .../08-tree-ppuzzle_5.3~rc16+dfsg-12build1_armhf.deb ... 237s Unpacking tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 237s Selecting previously unselected package tree-puzzle. 237s Preparing to unpack .../09-tree-puzzle_5.3~rc16+dfsg-12build1_armhf.deb ... 237s Unpacking tree-puzzle (5.3~rc16+dfsg-12build1) ... 237s Selecting previously unselected package tree-puzzle-doc. 237s Preparing to unpack .../10-tree-puzzle-doc_5.3~rc16+dfsg-12build1_all.deb ... 237s Unpacking tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 237s Setting up libslurm42t64 (24.11.1-1) ... 237s Setting up libhwloc15:armhf (2.12.0-1) ... 237s Setting up tree-puzzle-doc (5.3~rc16+dfsg-12build1) ... 237s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 237s Setting up libmpich12:armhf (4.2.1-5) ... 237s Setting up libsprng2 (2.0a-16) ... 237s Setting up tree-puzzle (5.3~rc16+dfsg-12build1) ... 237s Setting up hwloc-nox (2.12.0-1) ... 237s Setting up mpich (4.2.1-5) ... 237s update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode 237s update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode 237s Setting up mpi-default-bin (1.18) ... 237s Setting up tree-ppuzzle (5.3~rc16+dfsg-12build1) ... 237s Processing triggers for man-db (2.13.0-1) ... 238s Processing triggers for libc-bin (2.41-1ubuntu2) ... 250s autopkgtest [18:11:29]: test run-unit-test: [----------------------- 252s .: 252s EF.3trees 252s EF.phy 252s atp6.a 252s globin.a 252s globin.ctrees 252s globin.trees 252s marswolf.ctrees 252s marswolf.n 252s marswolf.trees 252s primates.b 252s primates.ctrees 252s primates.trees 252s tests 252s 252s ./tests: 252s build-puzzle.log 252s build-puzzle.trs 252s build-remark.log 252s build-remark.trs 252s check-cons-pure-prot 252s check-lm-pure-prot 252s check-qp-clock 252s check-qp-hky-clock-nucl 252s check-qp-hky-rhet-clock-nucl 252s check-qp-hky-rhet-nucl 252s check-qp-jtt-prot 252s check-qp-jtt-rhet-clock-prot 252s check-qp-jtt-rhet-prot 252s check-qp-mtrev-prot 252s check-qp-pure-bin 252s check-qp-pure-nucl 252s check-qp-pure-prot 252s check-qp-tn-nucl 252s check-qp-vt-prot 252s check-qp-wag-prot 252s check-ut-pure-prot 252s cons-pure-prot.ctrees 252s cons-pure-prot.log 252s cons-pure-prot.param 252s cons-pure-prot.prot 252s cons-pure-prot.test 252s cons-pure-prot.trs 252s generate-scripts.sh 252s lm-pure-prot.log 252s lm-pure-prot.param 252s lm-pure-prot.prot 252s lm-pure-prot.test 252s lm-pure-prot.trs 252s qp-clock.log 252s qp-clock.nucl 252s qp-clock.param 252s qp-clock.test 252s qp-clock.trs 252s qp-hky-clock-nucl.log 252s qp-hky-clock-nucl.nucl 252s qp-hky-clock-nucl.param 252s qp-hky-clock-nucl.test 252s qp-hky-clock-nucl.trs 252s qp-hky-rhet-clock-nucl.log 252s qp-hky-rhet-clock-nucl.nucl 252s qp-hky-rhet-clock-nucl.param 252s qp-hky-rhet-clock-nucl.test 252s qp-hky-rhet-clock-nucl.trs 252s qp-hky-rhet-nucl.log 252s qp-hky-rhet-nucl.nucl 252s qp-hky-rhet-nucl.param 252s qp-hky-rhet-nucl.test 252s qp-hky-rhet-nucl.trs 252s qp-jtt-prot.log 252s qp-jtt-prot.param 252s qp-jtt-prot.prot 252s qp-jtt-prot.test 252s qp-jtt-prot.trs 252s qp-jtt-rhet-clock-prot.log 252s qp-jtt-rhet-clock-prot.param 252s qp-jtt-rhet-clock-prot.prot 252s qp-jtt-rhet-clock-prot.test 252s qp-jtt-rhet-clock-prot.trs 252s qp-jtt-rhet-prot.log 252s qp-jtt-rhet-prot.param 252s qp-jtt-rhet-prot.prot 252s qp-jtt-rhet-prot.test 252s qp-jtt-rhet-prot.trs 252s qp-mtrev-prot.log 252s qp-mtrev-prot.param 252s qp-mtrev-prot.prot 252s qp-mtrev-prot.test 252s qp-mtrev-prot.trs 252s qp-pure-bin.bin 252s qp-pure-bin.log 252s qp-pure-bin.param 252s qp-pure-bin.test 252s qp-pure-bin.trs 252s qp-pure-nucl.log 252s qp-pure-nucl.nucl 252s qp-pure-nucl.param 252s qp-pure-nucl.test 252s qp-pure-nucl.trs 252s qp-pure-prot.log 252s qp-pure-prot.param 252s qp-pure-prot.prot 252s qp-pure-prot.test 252s qp-pure-prot.trs 252s qp-tn-nucl.log 252s qp-tn-nucl.nucl 252s qp-tn-nucl.param 252s qp-tn-nucl.test 252s qp-tn-nucl.trs 252s qp-vt-prot.log 252s qp-vt-prot.param 252s qp-vt-prot.prot 252s qp-vt-prot.test 252s qp-vt-prot.trs 252s qp-wag-prot.log 252s qp-wag-prot.param 252s qp-wag-prot.prot 252s qp-wag-prot.test 252s qp-wag-prot.trs 252s template-test 252s test-suite.log 252s ut-pure-prot.log 252s ut-pure-prot.param 252s ut-pure-prot.prot 252s ut-pure-prot.test 252s ut-pure-prot.trees 252s ut-pure-prot.trs 252s Test 1 252s WARNING: random seed set to 1001 for debugging! 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-pure-bin.bin' 252s Input file: tests/qp-pure-bin.bin 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-pure-bin.bin) contains 5 sequences of length 895 252s 1. Gibbon 252s 2. Human 252s 3. Chimpanzee 252s 4. Gorilla 252s 5. Orangutan 252s (consists very likely of binary state data) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Exact maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Gibbon (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Binary states 252s m Model of substitution? Two-state model (Felsenstein 1981) 252s f Binary state frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Exact maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Gibbon (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Exact maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Gibbon (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Def.: JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Exact maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Gibbon (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Binary states 252s m Model of substitution? Two-state model (Felsenstein 1981) 252s f Binary state frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Writing parameters to file tests/qp-pure-bin.bin.puzzle 252s Writing parameters to file tests/qp-pure-bin.bin.puzzle 252s Writing pairwise distances to file tests/qp-pure-bin.bin.dist 252s Writing parameters to file tests/qp-pure-bin.bin.puzzle 252s Writing parameters to file tests/qp-pure-bin.bin.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s WARNING: random seed set to 1001 for debugging! 252s WARNING: random seed set to 1001 for debugging! 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-pure-bin.bin.puzzle 252s Likelihood distances: tests/qp-pure-bin.bin.dist 252s Phylip tree file: tests/qp-pure-bin.bin.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 2 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-pure-nucl.nucl' 252s Input file: tests/qp-pure-nucl.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-pure-nucl.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing substitution process parameters 252s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 252s Writing pairwise distances to file tests/qp-pure-nucl.nucl.dist 252s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-pure-nucl.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-pure-nucl.nucl.puzzle 252s Likelihood distances: tests/qp-pure-nucl.nucl.dist 252s Phylip tree file: tests/qp-pure-nucl.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 3 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-tn-nucl.nucl' 252s Input file: tests/qp-tn-nucl.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-tn-nucl.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? TN (Tamura-Nei 1993) 252s p Constrain TN model to F84 model? No 252s t Transition/transversion parameter? Estimate from data set 252s r Y/R transition parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing substitution process parameters 252s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 252s Writing pairwise distances to file tests/qp-tn-nucl.nucl.dist 252s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-tn-nucl.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-tn-nucl.nucl.puzzle 252s Likelihood distances: tests/qp-tn-nucl.nucl.dist 252s Phylip tree file: tests/qp-tn-nucl.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 4 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-hky-clock-nucl.nucl' 252s Input file: tests/qp-hky-clock-nucl.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s WARNING: random seed set to 1001 for debugging! 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-hky-clock-nucl.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? Yes 252s l Location of root? Best place (automatic search) 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing substitution process parameters 252s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 252s Writing pairwise distances to file tests/qp-hky-clock-nucl.nucl.dist 252s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-clock-nucl.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s Computing maximum likelihood branch lengths (with clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-hky-clock-nucl.nucl.puzzle 252s Likelihood distances: tests/qp-hky-clock-nucl.nucl.dist 252s Phylip tree file: tests/qp-hky-clock-nucl.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s WARNING: random seed set to 1001 for debugging! 252s Passed 252s 252s Test 5 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-hky-rhet-nucl.nucl' 252s Input file: tests/qp-hky-rhet-nucl.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-hky-rhet-nucl.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Gamma distributed rates 252s a Gamma distribution parameter alpha? Estimate from data set 252s c Number of Gamma rate categories? 4 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 252s Writing pairwise distances to file tests/qp-hky-rhet-nucl.nucl.dist 252s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-rhet-nucl.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-hky-rhet-nucl.nucl.puzzle 252s Likelihood distances: tests/qp-hky-rhet-nucl.nucl.dist 252s Phylip tree file: tests/qp-hky-rhet-nucl.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 6 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-hky-rhet-clock-nucl.nucl' 252s Input file: tests/qp-hky-rhet-clock-nucl.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-hky-rhet-clock-nucl.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? Yes 252s l Location of root? Best place (automatic search) 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? Yes 252s l Location of root? Best place (automatic search) 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Gamma distributed rates 252s a Gamma distribution parameter alpha? Estimate from data set 252s c Number of Gamma rate categories? 4 252s 252s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 252s 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Optimizing missing substitution process parameters 252s Optimizing missing rate heterogeneity parameters 252s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 252s Writing pairwise distances to file tests/qp-hky-rhet-clock-nucl.nucl.dist 252s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 252s Writing parameters to file tests/qp-hky-rhet-clock-nucl.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s Computing maximum likelihood branch lengths (with clock) 252s WARNING: random seed set to 1001 for debugging! 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-hky-rhet-clock-nucl.nucl.puzzle 252s Likelihood distances: tests/qp-hky-rhet-clock-nucl.nucl.dist 252s Phylip tree file: tests/qp-hky-rhet-clock-nucl.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 7 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-pure-prot.prot' 252s Input file: tests/qp-pure-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-pure-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Writing parameters to file tests/qp-pure-prot.prot.puzzle 252s Writing parameters to file tests/qp-pure-prot.prot.puzzle 252s Writing pairwise distances to file tests/qp-pure-prot.prot.dist 252s Writing parameters to file tests/qp-pure-prot.prot.puzzle 252s Writing parameters to file tests/qp-pure-prot.prot.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-pure-prot.prot.puzzle 252s Likelihood distances: tests/qp-pure-prot.prot.dist 252s Phylip tree file: tests/qp-pure-prot.prot.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 8 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-mtrev-prot.prot' 252s Input file: tests/qp-mtrev-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s WARNING: random seed set to 1001 for debugging! 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-mtrev-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 252s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 252s Writing pairwise distances to file tests/qp-mtrev-prot.prot.dist 252s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 252s Writing parameters to file tests/qp-mtrev-prot.prot.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-mtrev-prot.prot.puzzle 252s Likelihood distances: tests/qp-mtrev-prot.prot.dist 252s Phylip tree file: tests/qp-mtrev-prot.prot.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 9 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-vt-prot.prot' 252s Input file: tests/qp-vt-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s WARNING: random seed set to 1001 for debugging! 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-vt-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? VT (Mueller-Vingron 2000) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Writing parameters to file tests/qp-vt-prot.prot.puzzle 252s Writing parameters to file tests/qp-vt-prot.prot.puzzle 252s Writing pairwise distances to file tests/qp-vt-prot.prot.dist 252s Writing parameters to file tests/qp-vt-prot.prot.puzzle 252s Writing parameters to file tests/qp-vt-prot.prot.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-vt-prot.prot.puzzle 252s Likelihood distances: tests/qp-vt-prot.prot.dist 252s Phylip tree file: tests/qp-vt-prot.prot.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 10 252s WARNING: random seed set to 1001 for debugging! 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-wag-prot.prot' 252s Input file: tests/qp-wag-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-wag-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? mtREV24 (Adachi-Hasegawa 1996) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? BLOSUM62 (Henikoff-Henikoff 92) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? VT (Mueller-Vingron 2000) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? WAG (Whelan-Goldman 2000) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Writing parameters to file tests/qp-wag-prot.prot.puzzle 252s Writing parameters to file tests/qp-wag-prot.prot.puzzle 252s Writing pairwise distances to file tests/qp-wag-prot.prot.dist 252s Writing parameters to file tests/qp-wag-prot.prot.puzzle 252s Writing parameters to file tests/qp-wag-prot.prot.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s WARNING: random seed set to 1001 for debugging! 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-wag-prot.prot.puzzle 252s Likelihood distances: tests/qp-wag-prot.prot.dist 252s Phylip tree file: tests/qp-wag-prot.prot.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 11 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-clock.nucl' 252s Input file: tests/qp-clock.nucl 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-clock.nucl) contains 8 sequences of length 116 252s 1. Thylacinus 252s 2. Sarcophilu 252s 3. Dasyurus 252s 4. Echymipera 252s 5. Trichosuru 252s 6. Phalanger 252s 7. Philander 252s 8. Bos 252s (consists very likely of nucleotides) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? Thylacinus (1) 252s z Compute clocklike branch lengths? Yes 252s l Location of root? Best place (automatic search) 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing substitution process parameters 252s Writing parameters to file tests/qp-clock.nucl.puzzle 252s Writing parameters to file tests/qp-clock.nucl.puzzle 252s Writing pairwise distances to file tests/qp-clock.nucl.dist 252s Writing parameters to file tests/qp-clock.nucl.puzzle 252s Writing parameters to file tests/qp-clock.nucl.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s Computing maximum likelihood branch lengths (with clock) 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-clock.nucl.puzzle 252s Likelihood distances: tests/qp-clock.nucl.dist 252s Phylip tree file: tests/qp-clock.nucl.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 12 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-jtt-prot.prot' 252s Input file: tests/qp-jtt-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-jtt-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: WARNING: random seed set to 1001 for debugging! 252s 252s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 252s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 252s Writing pairwise distances to file tests/qp-jtt-prot.prot.dist 252s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 252s Writing parameters to file tests/qp-jtt-prot.prot.puzzle 252s Computing quartet maximum likelihood trees 252s Computing quartet puzzling trees 252s Computing maximum likelihood branch lengths (without clock) 252s WARNING: random seed set to 1001 for debugging! 252s 252s All results written to disk: 252s Puzzle report file: tests/qp-jtt-prot.prot.puzzle 252s Likelihood distances: tests/qp-jtt-prot.prot.dist 252s Phylip tree file: tests/qp-jtt-prot.prot.tree 252s 252s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 252s Passed 252s 252s Test 13 252s 252s 252s 252s WELCOME TO TREE-PUZZLE 5.3.rc16! 252s 252s 252s 252s argv[1] = '-randseed1001' 252s argv[2] = 'tests/qp-jtt-rhet-prot.prot' 252s Input file: tests/qp-jtt-rhet-prot.prot 252s Using SPRNG -- Scalable Parallel Random Number Generator 252s RANDOM SEED: 1001 252s 252s Input data set (tests/qp-jtt-rhet-prot.prot) contains 7 sequences of length 128 252s 1. HBB_HUMAN 252s 2. HBB_HORSE 252s 3. HBA_HUMAN 252s 4. HBA_HORSE 252s 5. MYG_PHYCA 252s 6. GLB5_PETMA 252s 7. LGB2_LUPLU 252s (consists very likely of amino acids encoded on nuclear DNA) 252s 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Auto: Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Nucleotides 252s m Model of substitution? HKY (Hasegawa et al. 1985) 252s t Transition/transversion parameter? Estimate from data set 252s f Nucleotide frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Uniform rate 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s 252s 252s GENERAL OPTIONS 252s b Type of analysis? Tree reconstruction 252s k Tree search procedure? Quartet puzzling 252s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 252s n Number of puzzling steps? 1000 252s o Display as outgroup? HBB_HUMAN (1) 252s z Compute clocklike branch lengths? No 252s e Parameter estimates? Approximate (faster) 252s x Parameter estimation uses? Neighbor-joining tree 252s OUTPUT OPTIONS 252s 9 List puzzling trees/splits (NEXUS)? No 252s u List unresolved quartets? No 252s j List puzzling step trees? No 252s SUBSTITUTION PROCESS 252s d Type of sequence input data? Amino acids 252s m Model of substitution? JTT (Jones et al. 1992) 252s f Amino acid frequencies? Estimate from data set 252s RATE HETEROGENEITY 252s w Model of rate heterogeneity? Gamma distributed rates 252s a Gamma distribution parameter alpha? Estimate from data set 252s c Number of Gamma rate categories? 4 252s 252s Quit [q], confirm [y], or change [menu] settings: 252s Optimizing missing rate heterogeneity parameters 253s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 253s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 253s Writing pairwise distances to file tests/qp-jtt-rhet-prot.prot.dist 253s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 253s Writing parameters to file tests/qp-jtt-rhet-prot.prot.puzzle 253s Computing quartet maximum likelihood trees 253s Computing quartet puzzling trees 253s Computing maximum likelihood branch lengths (without clock) 253s 253s All results written to disk: 253s Puzzle report file: tests/qp-jtt-rhet-prot.prot.puzzle 253s Likelihood distances: tests/qp-jtt-rhet-prot.prot.dist 253s Phylip tree file: tests/qp-jtt-rhet-prot.prot.tree 253s 253s The parameter estimation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 253s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The computation took 1.00 seconds (= 0.02 minutes = 0.00 hours) 253s including input 1.00 seconds (= 0.02 minutes = 0.00 hours) 253s Passed 253s 253s Test 14 253s 253s 253s 253s WELCOME TO TREE-PUZZLE 5.3.rc16! 253s 253s 253s 253s argv[1] = '-randseed1001' 253s argv[2] = 'tests/qp-jtt-rhet-clock-prot.prot' 253s Input file: tests/qp-jtt-rhet-clock-prot.prot 253s Using SPRNG -- Scalable Parallel Random Number Generator 253s WARNING: random seed set to 1001 for debugging! 253s RANDOM SEED: 1001 253s 253s Input data set (tests/qp-jtt-rhet-clock-prot.prot) contains 7 sequences of length 128 253s 1. HBB_HUMAN 253s 2. HBB_HORSE 253s 3. HBA_HUMAN 253s 4. HBA_HORSE 253s 5. MYG_PHYCA 253s 6. GLB5_PETMA 253s 7. LGB2_LUPLU 253s (consists very likely of amino acids encoded on nuclear DNA) 253s 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Auto: Amino acids 253s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Nucleotides 253s m Model of substitution? HKY (Hasegawa et al. 1985) 253s t Transition/transversion parameter? Estimate from data set 253s f Nucleotide frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? JTT (Jones et al. 1992) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? Yes 253s l Location of root? Best place (automatic search) 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? JTT (Jones et al. 1992) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? Yes 253s l Location of root? Best place (automatic search) 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? JTT (Jones et al. 1992) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Gamma distributed rates 253s a Gamma distribution parameter alpha? Estimate from data set 253s c Number of Gamma rate categories? 4 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s Optimizing missing rate heterogeneity parameters 253s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 253s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 253s Writing pairwise distances to file tests/qp-jtt-rhet-clock-prot.prot.dist 253s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 253s Writing parameters to file tests/qp-jtt-rhet-clock-prot.prot.puzzle 253s Computing quartet maximum likelihood trees 253s Computing quartet puzzling trees 253s Computing maximum likelihood branch lengths (without clock) 253s Computing maximum likelihood branch lengths (with clock) 253s 253s All results written to disk: 253s Puzzle report file: tests/qp-jtt-rhet-clock-prot.prot.puzzle 253s Likelihood distances: tests/qp-jtt-rhet-clock-prot.prot.dist 253s Phylip tree file: tests/qp-jtt-rhet-clock-prot.prot.tree 253s 253s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The ML step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The puzzling step took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s Passed 253s 253s Test 15 253s WARNING: random seed set to 1001 for debugging! 253s 253s 253s 253s WELCOME TO TREE-PUZZLE 5.3.rc16! 253s 253s 253s 253s argv[1] = '-randseed1001' 253s argv[2] = 'tests/lm-pure-prot.prot' 253s Input file: tests/lm-pure-prot.prot 253s Using SPRNG -- Scalable Parallel Random Number Generator 253s RANDOM SEED: 1001 253s 253s Input data set (tests/lm-pure-prot.prot) contains 7 sequences of length 128 253s 1. HBB_HUMAN 253s 2. HBB_HORSE 253s 3. HBA_HUMAN 253s 4. HBA_HORSE 253s 5. MYG_PHYCA 253s 6. GLB5_PETMA 253s 7. LGB2_LUPLU 253s (consists very likely of amino acids encoded on nuclear DNA) 253s 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Auto: Amino acids 253s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Nucleotides 253s m Model of substitution? HKY (Hasegawa et al. 1985) 253s t Transition/transversion parameter? Estimate from data set 253s f Nucleotide frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Tree reconstruction 253s k Tree search procedure? Quartet puzzling 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s n Number of puzzling steps? 1000 253s o Display as outgroup? HBB_HUMAN (1) 253s z Compute clocklike branch lengths? No 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s OUTPUT OPTIONS 253s 9 List puzzling trees/splits (NEXUS)? No 253s u List unresolved quartets? No 253s j List puzzling step trees? No 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s 253s 253s GENERAL OPTIONS 253s b Type of analysis? Likelihood mapping 253s v Quartet evaluation criterion? Approximate maximum likelihood (ML) 253s g Group sequences in clusters? No 253s n Number of quartets? 35 (all possible) 253s e Parameter estimates? Approximate (faster) 253s x Parameter estimation uses? Neighbor-joining tree 253s SUBSTITUTION PROCESS 253s d Type of sequence input data? Amino acids 253s m Model of substitution? Auto: Dayhoff (Dayhoff et al. 1978) 253s f Amino acid frequencies? Estimate from data set 253s RATE HETEROGENEITY 253s w Model of rate heterogeneity? Uniform rate 253s 253s Quit [q], confirm [y], or change [menu] settings: 253s Writing parameters to file tests/lm-pure-prot.prot.puzzle 253s Writing parameters to file tests/lm-pure-prot.prot.puzzle 253s Writing pairwise distances to file tests/lm-pure-prot.prot.dist 253s Writing parameters to file tests/lm-pure-prot.prot.puzzle 253s Writing parameters to file tests/lm-pure-prot.prot.puzzle 253s Performing likelihood mapping analysis 253s PPP1: 0 (./puzzle1.c:8696) 253s 253s All results written to disk: 253s Puzzle report file: tests/lm-pure-prot.prot.puzzle 253s Likelihood distances: tests/lm-pure-prot.prot.dist 253s Likelihood mapping diagram (EPS): tests/lm-pure-prot.prot.eps 253s Likelihood mapping diagram (SVG): tests/lm-pure-prot.prot.svg 253s 253s The parameter estimation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s The computation took 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s including input 0.00 seconds (= 0.00 minutes = 0.00 hours) 253s PPP1: 1 (./puzzle1.c:8702) 253s Passed 253s 254s autopkgtest [18:11:33]: test run-unit-test: -----------------------] 258s autopkgtest [18:11:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 258s run-unit-test PASS 262s autopkgtest [18:11:41]: @@@@@@@@@@@@@@@@@@@@ summary 262s run-unit-test PASS