diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,6 +5,11 @@ ## Unreleased changes +## Version 0.3.3 + +- Fix test suites. + + ## Version 0.3.2 - Remove llvm dependency. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.2. +Version: 0.3.3. Reproducible evolution made easy.

@@ -90,9 +90,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -136,9 +136,9 @@ slynx concatenate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -157,9 +157,9 @@ slynx examine --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -179,9 +179,9 @@ slynx filter-rows --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -202,9 +202,9 @@ slynx filter-columns --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -305,9 +305,9 @@ slynx sub-sample --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -335,9 +335,9 @@ slynx translate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -360,9 +360,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -399,9 +399,9 @@ tlynx compare --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES @@ -428,9 +428,9 @@ tlynx examine --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -452,9 +452,9 @@ tlynx simulate --help - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] [-M|--condition-on-mrca] [-l|--lambda DOUBLE] @@ -491,9 +491,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.2. + ELynx Suite version 0.3.3. Developed by Dominik Schrempf. - Compiled on August 17, 2020, at 14:19 pm, UTC. + Compiled on August 18, 2020, at 08:07 am, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses diff --git a/data/ConnectA.tree b/data/ConnectA.tree new file mode 100644 --- /dev/null +++ b/data/ConnectA.tree @@ -0,0 +1,1 @@ +(1,(2,(3,(4,5)))); diff --git a/data/ConnectB.tree b/data/ConnectB.tree new file mode 100644 --- /dev/null +++ b/data/ConnectB.tree @@ -0,0 +1,1 @@ +(((((a,b),c),d),e),f); diff --git a/data/ConnectConstraints.tree b/data/ConnectConstraints.tree new file mode 100644 --- /dev/null +++ b/data/ConnectConstraints.tree @@ -0,0 +1,2 @@ +(a,b,c); +(1,2,3); diff --git a/data/Many.trees b/data/Many.trees new file mode 100644 --- /dev/null +++ b/data/Many.trees @@ -0,0 +1,104 @@ +(Alligator_mississippiensis:0.0526528081,Alligator_sinensis:0.0734637848,((Caiman_crocodilus:0.0969821137,(((((((((((Crocodylus_acutus:0.0041044851,Crocodylus_intermedius:0.0000010000)93:0.0040987469,(Crocodylus_niloticus:0.0042196134,Crocodylus_rhombifer:0.0082527754)57:0.0000010000)96:0.0137859140,Crocodylus_moreletii:0.0083237829)88:0.0186659597,Crocodylus_palustris:0.0311339573)66:0.0071136402,Crocodylus_mindorensis:0.0256926658)37:0.0041484246,Crocodylus_novaeguineae:0.0200863253)18:0.0041308153,(Crocodylus_porosus:0.0126862207,Crocodylus_siamensis:0.0045759540)74:0.0000010000)66:0.0322010915,Crocodylus_johnsoni:0.0336452822)69:0.0355435615,Mecistops_cataphractus:0.0527867124)19:0.0123373068,Osteolaemus_tetraspis:0.0488522786)45:0.0427941726,(Gavialis_gangeticus:0.0422921048,Tomistoma_schlegelii:0.0498460335)91:0.0523407887)100:0.2843610351)64:0.0296943427,(Paleosuchus_palpebrosus:0.0269905316,Paleosuchus_trigonatus:0.0619737812)100:0.0709999945)94:0.0428787784); +(Alligator_mississippiensis:0.0524740841,Alligator_sinensis:0.0800162019,((Caiman_crocodilus:0.0941235886,(((((((((((Crocodylus_acutus:0.0043175143,Crocodylus_intermedius:0.0000010000)86:0.0043344207,(Crocodylus_niloticus:0.0044760167,Crocodylus_rhombifer:0.0086874162)65:0.0000010000)95:0.0166796281,Crocodylus_moreletii:0.0060421344)87:0.0213806656,Crocodylus_palustris:0.0324075223)54:0.0054115732,Crocodylus_mindorensis:0.0274494966)47:0.0044391248,Crocodylus_novaeguineae:0.0213756693)20:0.0043300941,Crocodylus_siamensis:0.0047931398)11:0.0000010000,Crocodylus_porosus:0.0135779878)63:0.0313862462,Crocodylus_johnsoni:0.0358113254)67:0.0368328022,((Gavialis_gangeticus:0.0429862138,Tomistoma_schlegelii:0.0546944923)99:0.1013554525,Osteolaemus_tetraspis:0.0379567746)76:0.0182589653)39:0.0271711713,Mecistops_cataphractus:0.0272528658)100:0.3148076446)86:0.0261810374,(Paleosuchus_palpebrosus:0.0328170533,Paleosuchus_trigonatus:0.0595155628)99:0.0685486180)97:0.0465605886); +(Alligator_mississippiensis:0.0539821570,Alligator_sinensis:0.0830720003,((Caiman_crocodilus:0.0896735879,((((((((((Crocodylus_acutus:0.0043914732,Crocodylus_intermedius:0.0000010000)90:0.0044243990,(Crocodylus_niloticus:0.0045600536,Crocodylus_rhombifer:0.0088779570)62:0.0000010000)94:0.0171188139,Crocodylus_moreletii:0.0061979643)88:0.0226175086,Crocodylus_palustris:0.0337618013)50:0.0052814705,Crocodylus_mindorensis:0.0280485397)41:0.0045765944,Crocodylus_novaeguineae:0.0214014934)29:0.0044378220,(Crocodylus_porosus:0.0138428451,Crocodylus_siamensis:0.0051894136)58:0.0000010000)87:0.0315929596,Crocodylus_johnsoni:0.0374011213)87:0.0377642428,((Gavialis_gangeticus:0.0452826570,Tomistoma_schlegelii:0.0555076715)98:0.1064762805,Osteolaemus_tetraspis:0.0381804798)76:0.0192642145)53:0.0286304370,Mecistops_cataphractus:0.0302348706)100:0.3500571691)85:0.0312149387,(Paleosuchus_palpebrosus:0.0328834210,Paleosuchus_trigonatus:0.0603955588)98:0.0685505893)97:0.0492786281); +(Alligator_mississippiensis:0.0535743395,Alligator_sinensis:0.0860074123,((Caiman_crocodilus:0.0971952192,(((((((Crocodylus_acutus:0.0043890735,Crocodylus_intermedius:0.0000010000)91:0.0044039971,(Crocodylus_niloticus:0.0045223659,Crocodylus_rhombifer:0.0088277224)54:0.0000021403)94:0.0170178534,Crocodylus_moreletii:0.0061381134)84:0.0224165720,Crocodylus_palustris:0.0331891999)42:0.0057746050,Crocodylus_mindorensis:0.0281347628)36:0.0047295365,((Crocodylus_johnsoni:0.0360354557,(((Gavialis_gangeticus:0.0444005100,Tomistoma_schlegelii:0.0580010558)99:0.1089741040,Osteolaemus_tetraspis:0.0398566789)79:0.0188068117,Mecistops_cataphractus:0.0622380784)51:0.0379548565)42:0.0324838098,(Crocodylus_porosus:0.0138716650,Crocodylus_siamensis:0.0055618494)63:0.0000020752)16:0.0043992318)27:0.0102133073,Crocodylus_novaeguineae:0.0108028622)100:0.3950105303)80:0.0290990426,(Paleosuchus_palpebrosus:0.0358615795,Paleosuchus_trigonatus:0.0602743439)98:0.0722137283)96:0.0521273654); +(Alligator_mississippiensis:0.0541785831,Alligator_sinensis:0.0871756441,((Caiman_crocodilus:0.1011411666,(((((((Crocodylus_acutus:0.0044026937,Crocodylus_intermedius:0.0000010000)90:0.0044154193,(Crocodylus_niloticus:0.0045334548,Crocodylus_rhombifer:0.0088515851)67:0.0000010000)97:0.0171035049,Crocodylus_moreletii:0.0061726612)86:0.0224019818,Crocodylus_palustris:0.0332384064)52:0.0058314571,Crocodylus_mindorensis:0.0281966686)42:0.0047329296,((Crocodylus_johnsoni:0.0360209418,(((Gavialis_gangeticus:0.0448629917,Tomistoma_schlegelii:0.0585219193)98:0.1109694983,Osteolaemus_tetraspis:0.0402361937)81:0.0191069458,Mecistops_cataphractus:0.0623754978)53:0.0385465892)47:0.0328223237,(Crocodylus_porosus:0.0139077152,Crocodylus_siamensis:0.0055885752)66:0.0000010000)23:0.0044142156)38:0.0104487321,Crocodylus_novaeguineae:0.0105911453)100:0.4048406316)80:0.0270245932,(Paleosuchus_palpebrosus:0.0367659451,Paleosuchus_trigonatus:0.0601318898)98:0.0722126084)95:0.0527012652); 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a/data/MicrospoEDM32.tree b/data/MicrospoEDM32.tree new file mode 100644 --- /dev/null +++ b/data/MicrospoEDM32.tree @@ -0,0 +1,1 @@ 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diff --git a/data/MicrospoEDM64.tree b/data/MicrospoEDM64.tree new file mode 100644 --- /dev/null +++ b/data/MicrospoEDM64.tree @@ -0,0 +1,1 @@ 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diff --git a/data/MicrospoPoisson.tree b/data/MicrospoPoisson.tree new file mode 100644 --- /dev/null +++ b/data/MicrospoPoisson.tree @@ -0,0 +1,1 @@ 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diff --git a/data/Multifurcating.tree b/data/Multifurcating.tree new file mode 100644 --- /dev/null +++ b/data/Multifurcating.tree @@ -0,0 +1,1 @@ 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diff --git a/data/Newick.tree b/data/Newick.tree new file mode 100644 --- /dev/null +++ b/data/Newick.tree @@ -0,0 +1,1 @@ 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diff --git a/data/NewickConstraint.tree b/data/NewickConstraint.tree new file mode 100644 --- /dev/null +++ b/data/NewickConstraint.tree @@ -0,0 +1,1 @@ 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diff --git a/data/NewickRevBayes.tree b/data/NewickRevBayes.tree new file mode 100644 --- /dev/null +++ b/data/NewickRevBayes.tree @@ -0,0 +1,1 @@ 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diff --git a/data/NewickRooted.tree b/data/NewickRooted.tree new file mode 100644 --- /dev/null +++ b/data/NewickRooted.tree @@ -0,0 +1,1 @@ 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b/data/SimpleTree.nex new file mode 100644 --- /dev/null +++ b/data/SimpleTree.nex @@ -0,0 +1,4 @@ +#NEXUS +BEGIN TREES; + TREE tree1 = ((A,B),C); +END; diff --git a/data/TreeDist.trees b/data/TreeDist.trees new file mode 100644 --- /dev/null +++ b/data/TreeDist.trees @@ -0,0 +1,3 @@ +((A,C),(D,(B,E))); +(((A,D),C),(B,E)); +(((A:0.1,D:0.25):0.05,C:0.01):0.2,(B:0.3,E:0.8):0.2); diff --git a/data/UltraMetric.log b/data/UltraMetric.log new file mode 100644 --- /dev/null +++ b/data/UltraMetric.log @@ -0,0 +1,22 @@ +--------------------------------------------------------------- +-- Simulate phylogenetic trees using birth and death processes. +ELynx Suite version 0.0.1. +Developed by Dominik Schrempf. +Compiled on January 13, 2020, at 16:42 pm, UTC. +Start time: January 14, 2020, at 09:35 am, UTC. +Command line: tlynx -o UltraMetric simulate -t 1 -n 10 -H 1.0 +-- Arguments +Number of simulated trees: 1 +Number of leaves per tree: 10 +Height of trees: 1.0, conditioned on origin +Birth rate: 1.0 +Death rate: 0.9 +Sampling probability: 1.0 +Perform sub-sampling: False +Summary statistics only: False +Seed: Random +-- Simulation +Number of used cores: 4 +Write simulated trees to file 'UltraMetric.tree'. +-- End time: January 14, 2020, at 09:35 am, UTC. +------------------------------------------------ diff --git a/data/UltraMetric.tree b/data/UltraMetric.tree new file mode 100644 --- /dev/null +++ b/data/UltraMetric.tree @@ -0,0 +1,1 @@ +(((0:0.15701835735846079,1:0.15701835735846079)0:0.652885950565262,(((2:6.10600573606971e-2,3:6.10600573606971e-2)0:9.78964778037197e-2,4:0.1589565351644168)0:0.2596879494356997,(5:0.3597001373542192,(6:0.2253255757754673,7:0.2253255757754673)0:0.13437456157875188)0:5.8944347245897366e-2)0:0.3912598233236063)0:0.18910205484970333,(8:0.35058502500045813,9:0.35058502500045813)0:0.648421337772968)0:9.936372265738624e-4; diff --git a/elynx-tree.cabal b/elynx-tree.cabal --- a/elynx-tree.cabal +++ b/elynx-tree.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: elynx-tree -version: 0.3.2 +version: 0.3.3 synopsis: Handle phylogenetic trees description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at . category: Bioinformatics @@ -16,6 +16,23 @@ extra-source-files: README.md ChangeLog.md + data/ConnectA.tree + data/ConnectB.tree + data/ConnectConstraints.tree + data/Many.trees + data/MicrospoEDM32.tree + data/MicrospoEDM64.tree + data/MicrospoPoisson.tree + data/Multifurcating.tree + data/NewickConstraint.tree + data/NewickRevBayes.tree + data/NewickRooted.tree + data/Newick.tree + data/RevBayes.trees + data/SimpleTree.nex + data/TreeDist.trees + data/UltraMetric.log + data/UltraMetric.tree source-repository head type: git