{"id":16300223,"url":"https://github.com/rvosa/bio-phylo","last_synced_at":"2025-09-04T19:49:25.557Z","repository":{"id":65218621,"uuid":"1560824","full_name":"rvosa/bio-phylo","owner":"rvosa","description":"Bio::Phylo - Phyloinformatic analysis using Perl","archived":false,"fork":false,"pushed_at":"2019-05-31T14:19:17.000Z","size":81049,"stargazers_count":16,"open_issues_count":3,"forks_count":6,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-02-28T23:21:03.554Z","etag":null,"topics":["bioinformatics","computational-biology","evolution","perl","phylogenetics","toolkit"],"latest_commit_sha":null,"homepage":"http://search.cpan.org/dist/Bio-Phylo","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rvosa.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2011-04-02T20:58:14.000Z","updated_at":"2023-12-06T08:41:55.000Z","dependencies_parsed_at":"2023-01-16T14:52:30.861Z","dependency_job_id":null,"html_url":"https://github.com/rvosa/bio-phylo","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rvosa%2Fbio-phylo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rvosa%2Fbio-phylo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rvosa%2Fbio-phylo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rvosa%2Fbio-phylo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rvosa","download_url":"https://codeload.github.com/rvosa/bio-phylo/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244056404,"owners_count":20390719,"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":["bioinformatics","computational-biology","evolution","perl","phylogenetics","toolkit"],"created_at":"2024-10-10T20:50:39.876Z","updated_at":"2025-03-20T05:31:04.636Z","avatar_url":"https://github.com/rvosa.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"![](https://raw.githubusercontent.com/rvosa/bio-phylo/master/banner.png)\n\nBio::Phylo\n==========\n\nAn object-oriented toolkit for analyzing and manipulating phyloinformatic data. \n\nDESCRIPTION\n-----------\nPhylogenetics is the branch of evolutionary biology that deals with reconstructing and \nanalyzing the tree of life. This distribution provides objects and methods to aid in \nhandling and analyzing phylogenetic data.\n\nCOMPATIBILITY\n-------------\nBio::Phylo installs without problems on most popular, current platforms (Win32, OSX, \nLinux, Solaris, IRIX, FreeBSD, OpenBSD, NetBSD), on Perl versions \u003e= 5.8.0\n\nFor a list of automated test results for the latest release number visit:\n\nhttp://testers.cpan.org/show/Bio-Phylo.html\n\nCurrently, the build status at Travis for the head revision is:\n\n[![Build Status](https://travis-ci.org/rvosa/bio-phylo.svg?branch=master)](https://travis-ci.org/rvosa/bio-phylo)\n\nINSTALLATION\n------------\nBio::Phylo has no dependencies for its core install. However, some additional \nfunctionality will not work (e.g. XML parsing) until the CPAN module that enables \nit has been installed (e.g. XML::Twig). You can install these at a later date if \nand when need arises. For example, when you get an error message at runtime that \nalerts you to a missing dependency. If any of such additional CPAN modules are \nfound to be missing at installation time, a warning will be emitted, but \ninstallation and unit testing can continue.\n\nTo install the Bio::Phylo distribution itself, run the following commands: \n\n    perl Makefile.PL\n    make\n    make test # Optional, runs unit tests, which should pass\n    make install\n \n(For platform specific information on what 'make' command to use, check \"perl -V:make\". \nOn Windows this usually returns \"make='nmake';\", which means you'll need the free 'nmake' \nutility)\n\nCONTRIBUTORS\n------------\nThe following people have contributed code to the project:\n* Rutger Vos\n* Hannes Hettling\n* Florent Angly\n* Jason Caravas\n* Klaas Hartmann\n* Mark A. Jensen\n* Moritz Lenz\n* Chase Miller\n* Aki Mimoto\n* Jan Willem Wijnands\n\nThe following people have provided feedback through issues and reviews:\n* Denis Baurain\n* Chris Fields\n* Shlomi Fish\n* Jean-Marc Frigerio\n* Andreas J. König\n* Hilmar Lapp\n* Nicolas Lenfant\n* Sébastien Moretti\n* Slaven Rezić\n* `Seiler`\n* `scorpio17`\n\nBUGS\n----\nPlease report any bugs or feature requests on the GitHub bug tracker:\n\nhttps://github.com/rvosa/bio-phylo/issues\n \nACKNOWLEDGEMENTS\n----------------\nThe authors would like to thank the BioPerl project for providing the community\nwith a terrific toolkit that other software, such as this, can be built on\n(http://www.bioperl.org); and Arne Mooers from the FAB* lab (http://www.sfu.ca/~fabstar) \nfor comments and requests.\n\nThe research leading to these results has received funding from the European\nCommunity's Seventh Framework Programme (FP7/2007-2013) under grant agreement\nno. 237046.\n\nSEE ALSO\n--------\n**Documentation** This distribution contains a high-level overview that can be \naccessed using the perldoc documentation system. The documentation is at \n[Bio::Phylo::Manual](lib/Bio/Phylo/Manual.pod) and can be viewed (after \ninstallation) on the command line:\n\n    perldoc Bio::Phylo::Manual\n\n**Optional extensions** Compatible with this distribution are two optional \npackages that can be installed alongside Bio::Phylo. These packages are:\n- [Bio::PhyloXS](http://search.cpan.org/dist/Bio-PhyloXS/) - which provides \n  faster implementations (in C) of the core objects of Bio::Phylo. The source\n  code repository is [here](https://github.com/rvosa/bio-phylo-xs), and the\n  v0.1.0 release is tagged as \n  [10.5281/zenodo.1010362](http://doi.org/10.5281/zenodo.1010362).\n- [Bio::Phylo::Forest::DBTree](http://search.cpan.org/dist/Bio-Phylo-Forest-DBTree/) -\n  which provides an object-relational mapping of the core objects of Bio::Phylo.\n  The source code repository is \n  [here](https://github.com/rvosa/bio-phylo-forest-dbtree), and the v0.1.2\n  release is tagged as \n  [10.5281/zenodo.1035856](http://doi.org/10.5281/zenodo.1035856).\n\nCITATION\n--------\nIf you use Bio::Phylo in published research, please cite it:\n\n**Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen\nand Chase Miller**, 2011. Bio::Phylo - phyloinformatic analysis using Perl.\n_BMC Bioinformatics_ 12:63.\ndoi:[10.1186/1471-2105-12-63](http://doi.org/10.1186/1471-2105-12-63)\n\nCOPYRIGHT \u0026 LICENSE\n-------------------\nCopyright 2005-2017 Rutger Vos, All Rights Reserved. This program is free software; \nyou can redistribute it and/or modify it under the same terms as Perl itself, i.e.\na choice between the following licenses:\n- [The Artistic License](COPYING)\n- [GNU General Public License v3.0](LICENSE)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frvosa%2Fbio-phylo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frvosa%2Fbio-phylo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frvosa%2Fbio-phylo/lists"}