{"id":20714667,"url":"https://github.com/fabsta/hieranoid","last_synced_at":"2025-04-23T10:33:55.724Z","repository":{"id":5785912,"uuid":"6999983","full_name":"fabsta/Hieranoid","owner":"fabsta","description":null,"archived":false,"fork":false,"pushed_at":"2013-08-15T21:43:34.000Z","size":14892,"stargazers_count":7,"open_issues_count":2,"forks_count":5,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-29T23:22:29.242Z","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":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fabsta.png","metadata":{"files":{"readme":"README","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":"2012-12-04T12:58:52.000Z","updated_at":"2022-04-07T18:37:54.000Z","dependencies_parsed_at":"2022-09-02T15:30:52.881Z","dependency_job_id":null,"html_url":"https://github.com/fabsta/Hieranoid","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabsta%2FHieranoid","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabsta%2FHieranoid/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabsta%2FHieranoid/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fabsta%2FHieranoid/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fabsta","download_url":"https://codeload.github.com/fabsta/Hieranoid/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250417379,"owners_count":21427206,"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":"2024-11-17T02:33:27.506Z","updated_at":"2025-04-23T10:33:55.702Z","avatar_url":"https://github.com/fabsta.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"Hieranoid\nHierarchical orthology inference\n\nThis software is freely available at https://github.com/fabsta/Hieranoid \n\nPlease read the COPYING file before using this software.  \n\nIf you use Hieranoid please cite:\nFabian Schreiber and Erik L.L. Sonnhammer\nHieranoid: Hierarchical orthology inference \nJournal of Molecular Biology (submitted)\n\n\nInstallation\nChecking system requirements\n-\tPerl\n-\tBioPerl\n-\tUsearch or Blastall\n-\tHHSearch\n-\tMuscle or Kalign\n\nBe advised\nPerl, BioPerl, Blastall, Muscle and Kalign can be installed with 'apt-get install' command\nHHsearch and Usearch need to be installed manually\n\nPerl modules\nHieranoid uses Perl modules that are installed in the 'lib' sub-directory of the Hieranoid installation.\nPlease add that directory to your PERL5LIB enviromental variable. In bash you do that the following way:\n\texport PERL5LIB=$PERL5LIB:hieranoid_directory/lib\n\t\nBe advised \nFor cluster users, several Perl modules need to be install manually, possibly including:\nModule::Implementation\tModule::Runtime\nClass:Load\tClass:MOP\nSub::Exporter\tSub::Install\tSub::Name\nTry::Tiny\nPackage::DeprecationManager\tPackage::Stash\nMoose\nClone\nData::OptList\nParams::Util\n\nConfiguring Hieranoid\nOnce you have downloaded Hieranoid, you have to tell Hieranoid where to find the required programs. \nThis is done by adapting the settings in the Configuration file (Configurations/Configuration.pm).\nAll options should be explained in greater detail in the Configuration file\n\n\nStarting hieranoid\nOnce, the configuration file has been adapted, the analysis can be started by typing:\n\tperl hieranoid.pl\n\nNote that depending on the input size, the analysis can take some time\n\n\nCommand line arguments\nAdditional options:\n\t-c configurationFile\n\t-t guide tree file\n\n\nTest dataset:\nTo test the installation, simply type “perl hieranoid.pl”.\nThis will run a quick analysis on the sequences in data/sequences\nusing species tree in data/tree.\nProgram output:\nAll program output is stored in a directory ‘project1’. For each inner node of the provided species tree, a folder will be created in ‘project1/nodes’.\nThose folders contain several files: The input query files (e.g. Homo_sapiens.fa), Blast results (e.g. Homo_sapiens-Pan_troglodytes), the InParanoid output (sqltable.Homininae) and the orthology predictions (e.g. Homininae.OGTree.txt).\n\nWhere to put my files:\nHieranoid requires a set of sequences as well as a guide tree. By default the Hieranoid searches for the sequences in data/sequences and for the guide tree\nin data/tree. These options can be changed in the Configuration file.\n\n\nOutput:\nThe following is an example of the Hieranoid output format:\nHieranoidOG-Eukaryota3:((At1g50030.1:1.000,((ENSPTRP00000000280:1.000,ENSP00000354558:1.000)Homininae1:1.000,ENSMUSP00000099510:1.000)Euarchontoglires1:1.000)Eukaryota3:1.000)root;\nThe first is the name of the Hieranoid group followed by a newick string with inparalog scores\n \n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabsta%2Fhieranoid","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffabsta%2Fhieranoid","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffabsta%2Fhieranoid/lists"}