{"id":25977618,"url":"https://github.com/nylander/pmraic","last_synced_at":"2025-03-05T04:38:44.544Z","repository":{"id":3348368,"uuid":"4393218","full_name":"nylander/pMrAIC","owner":"nylander","description":"Parallel MrAIC","archived":false,"fork":false,"pushed_at":"2020-03-24T15:17:15.000Z","size":34,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-03-24T03:25:16.685Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"IPPETAD/code-2015","license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nylander.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2012-05-21T12:17:16.000Z","updated_at":"2020-03-24T15:17:17.000Z","dependencies_parsed_at":"2022-08-20T15:40:57.822Z","dependency_job_id":null,"html_url":"https://github.com/nylander/pMrAIC","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FpMrAIC","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FpMrAIC/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FpMrAIC/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2FpMrAIC/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nylander","download_url":"https://codeload.github.com/nylander/pMrAIC/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241966988,"owners_count":20050324,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-05T04:38:43.954Z","updated_at":"2025-03-05T04:38:44.530Z","avatar_url":"https://github.com/nylander.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"pMrAIC - Parallel MrAIC\n======\n\n\nNAME\n\n    pmraic.pl\n\n\nVERSION\n\n    Documentation for pmraic.pl version 1.1\n\n\nSYNOPSIS\n\n    pmraic.pl [options] FILE\n\n\nDESCRIPTION\n\n    Script for running nucleotide substitutions using PHYML (Guindon \u0026\n    Gasquel, 2003) in parallel. It will report the best AIC, AICc, BIC\n    model(s), along with the best ML tree under that/those models, and also\n    the syntax for specifying the model(s) in MrBayes v.3 (Ronquist \u0026\n    Huelsenbeck, 2003).\n\n\nOPTIONS\n\n    Mandatory arguments to long options are mandatory for short options too\n\n    -b, --bash=*number*\n            Generate *number* of bash scripts for running PHYML. Can be\n            manually distributed to several machines. Use *--summarize*\n            later for collecting the output. Using this option will not\n            start PHYML, but the analyses have to be started manually (using\n            the scripts).\n\n    -c, --cpu=*number*\n            Number of \"CPUs\" to use. Default is to run as many as the number\n            of available cores.\n\n    -i, --infile=*infile*\n            Excplicitly specify the *infile* to be used. The infile should\n            have nt sequences and be readable by phyml.\n\n    -mau, --maui\n            Create submit files for the Maui cluster scheduler system. Use\n            *--summarize* later for collecting the output.\n\n    -models, --models=*arg1,arg2,...,argn*\n            Specify a subset of the 56 models available to be run by PHYML.\n            *arg1,arg2,...,argn* should be given as a comma-separated list.\n            No spaces. Note that a MrBayes block will only be printed if the\n            best model is among the 24 nt models available in MrBayes v.3.\n            Valid model names are (first 24 are available in MrBayes):\n\n                F81,F81G,F81I,F81IG,GTR,GTRG,\n                GTRI,GTRIG,HKY85,HKY85G,HKY85I,HKY85IG,\n                JC69,JC69G,JC69I,JC69IG,K2P,K2PG,\n                K2PI,K2PIG,SYM,SYMG,SYMI,SYMIG\n\n                K3P,K3PG,K3PI,K3PIG,K3PUF,K3PUFG,\n                K3PUFI,K3PUFIG,TIM,TIMEF,TIMEFG,TIMEFI,\n                TIMEFIG,TIMG,TIMI,TIMIG,TRN,TRNEF,\n                TRNEFG,TRNEFI,TRNEFIG,TRNG,TRNI,TRNIG,\n                TVM,TVMEF,TVMEFG,TVMEFI,TVMEFIG,TVMG,\n                TVMI,TVMIG,\n\n    -modelt, --modeltest\n            Run all 56 models.\n\n    -o, --optimize=*arg*\n            Specify the optimizing *arg* for phyml. One of the following are\n            allowed: *tlr*, *tl*, *lr*, *l*, *r*, or *n*. Default is *tlr*,\n            optimize all.\n\n    -p, --phyml=*arg*\n            Specify the *PATH* to the phyml binary to be used. Good to use\n            when creating files for the Maui batch system or for running\n            files on remote systems. The default path for phyml is otherwise\n            taken from the users current PATH.\n\n    -se, --search=*arg*\n            Specify the search *arg* for phyml. One of the following are\n            allowed: *NNI*, *SPR*, or *BEST*. Default is *NNI*, the default\n            in phyml.\n\n    -su, --summarize\n            Summarize the output from pmraic.pl/phyml. Can also be set to\n            --nosummarize.\n\n    -v, --verbose\n            Be verbose. Can also be set to --noverbose.\n\n    -h, --help\n            Prints help message and exits\n\n    -v, --version\n            Prints version message and exits\n\n    -man, --man\n            Displays the manual page\n\n\nUSAGE\n\n    Examples:\n\n    Run PHYML in parallel. Default is to start as many different runs as\n    number of cores available\n\n        pmraic.pl data.dat\n\n    Run PHYML in parallel and without asking for user input\n\n        pmraic.pl --noverbose data.dat\n\n    Run two instances of PHYML in parallel (12 serial PHYML runs per CPU)\n\n        pmraic.pl --cpu=2 data.dat\n\n    Generate six bash scripts for running serial (6X4) PHYML analyses.\n\n        pmraic.pl --bash=6 data.dat\n\n    Generate a Maui submit script for running PHYML on a cluster\n\n        pmraic.pl --maui --phyml=/path/on/cluster/to/phyml data.dat\n\n    Run four models in parallel\n\n        pmraic.pl --models=JC69,JC69I,JC69G,JC69IG data.dat\n\n    Run 56 models (the \"Modeltest\" set) in parallel\n\n        pmraic.pl --modeltest data.dat\n\n    Summarize output from previous run(s)\n\n        pmraic.pl --summarize data.dat\n\n\nAUTHOR\n\n    Written by Johan A. A. Nylander\n\n\nREPORTING BUGS\n\n    See DEPENDENCIES below.\n    Please report any further bugs to *jnylander @ users.sourceforge.net*.\n\n\nDEPENDENCIES\n\n    Needs PhyML v. \u003e 3.0 to run. Note that current precompiled versions of\n    PhyML (\"v3.0_360-500M\") available from\n    http://www.atgc-montpellier.fr/phyml/ contains a bug preventing \"I\"\n    models to be correctly analysed (alpha jointly estimated, even when not\n    supposed to). This might effect model evaluations, especially if the\n    program is used in \"toggle mode\". The bug seems to be fixed, however, in\n    latest versions (at least v.\"20110919\") available on\n    http://code.google.com/p/phyml/.\n\n    Install on Ubuntu Linux:\n\n        sudo apt install phyml\n\n    Uses Perl modules Pod::Usage, Parallel::ForkManager.\n\n    Install on Ubuntu Linux:\n\n      sudo apt install perl-doc libparallel-forkmanager-perl\n\n    or directly from CPAN:\n\n      sudo perl -MCPAN -e 'install Parallel::ForkManager'\n\n\nLICENSE AND COPYRIGHT\n\n    Copyright (c) 2009-2020 Johan Nylander\n                   \n    Permission is hereby granted, free of charge, to any person\n    obtaining a copy of this software and associated documentation\n    files (the \"Software\"), to deal in the Software without\n    restriction, including without limitation the rights to use,\n    copy, modify, merge, publish, distribute, sublicense, and/or\n    sell copies of the Software, and to permit persons to whom the\n    Software is furnished to do so, subject to the following\n    conditions:\n\n    The above copyright notice and this permission notice shall be\n    included in all copies or substantial portions of the Software.\n\n    THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND,\n    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES\n    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND\n    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT\n    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,\n    WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR\n    OTHER DEALINGS IN THE SOFTWARE.\n\n\nDOWNLOAD\n\n    https://github.com/nylander/pMrAIC\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fpmraic","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnylander%2Fpmraic","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fpmraic/lists"}