{"bugs":[],"categories":[{"categoryid":354,"name":"media-gfx","summary":"The media-gfx category contains graphics-related packages."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"a198e862478387fe37b4d232d51a3edb558cd3e0","committime":"2025-12-19T10:01:01","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"grobian@gentoo.org","authorname":"Fabian Groffen","body":"Bug: https:\/\/bugs.gentoo.org\/473598\nBug: https:\/\/bugs.gentoo.org\/720224\nSigned-off-by: Fabian Groffen ","commitid":"2d25fad95cbaa525c8945d8e582c749d49524f49","committime":"2025-12-19T09:25:43","packageid":46128,"repoid":1,"summary":"*\/*: drop *-linux keywords"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"b082176271c4f0d63a97962e4b75785991196236","committime":"2025-12-17T15:16:13","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"grobian@gentoo.org","authorname":"Fabian Groffen","body":"The arch and OS that matches it are obsolete.\n\nSigned-off-by: Fabian Groffen ","commitid":"0a7ffce789e36042bac35ea5e0b8b2b654e5b490","committime":"2025-12-17T15:07:23","packageid":46128,"repoid":1,"summary":"*: remove ppc-macos keyword"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4fef0acf1d7c13b0478ee885bdf8d54b571dd6f5","committime":"2023-12-02T05:16:47","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"7b7a0493bc6a756dcfad9e945acbc84222fb0f55","committime":"2023-12-02T04:41:31","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: fix configure checks for modern c"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f2979793991144637956e4225ce4d0235900c1a2","committime":"2023-06-09T15:16:56","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"arthurzam@gentoo.org","authorname":"Arthur Zamarin","body":"Signed-off-by: Arthur Zamarin ","commitid":"7aab8f0479f7707bd7e648e90805326d27d6d7ce","committime":"2023-06-03T14:46:35","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: destabilize for ~x86"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"ad1e72b8e24e184cebb642747af2c79721ee51ee","committime":"2022-11-19T05:01:48","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/879751\nSigned-off-by: David Seifert ","commitid":"d4d7228930146c4626f8da2c0fb68c788329eb6a","committime":"2022-11-19T04:45:55","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: regenerate configure script for clang 16"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"519dcc6aa45f4e974fb1fd938b30849a924cbb80","committime":"2022-04-26T05:48:08","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"9903e675f0c8a3017a51954e1f239bf4d4842b13","committime":"2022-04-26T05:33:34","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: drop unused toolchain-funcs"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"d84283c1e6cab70ef207b0e9cee4a3dd5ef0ad3b","committime":"2022-01-29T00:21:42","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Closes: https:\/\/bugs.gentoo.org\/690900\nCloses: https:\/\/bugs.gentoo.org\/810502\nCloses: https:\/\/bugs.gentoo.org\/814185\nSigned-off-by: David Seifert ","commitid":"8fe21c3fd5b5e7be60a75a09ba4b3ec4bad417bd","committime":"2022-01-29T00:00:14","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: fix build system and MPI"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"0da74f9e557ec388bdcfe974722f0f8c59012b4f","committime":"2019-12-11T00:25:48","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.81, Repoman-2.3.20\nSigned-off-by: David Seifert ","commitid":"b0b40d543fca146fa2907f8d8ca63970403a74f1","committime":"2019-12-10T23:48:25","packageid":46128,"repoid":1,"summary":"sci-biology\/tree-puzzle: Port to EAPI 7"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":46128,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"Signed-off-by: Robin H. Johnson ","commitid":"61b861acd7b49083dab687e133f30f3331cb7480","committime":"2017-02-28T19:47:27","packageid":46128,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":46128,"repoid":1,"summary":"2015-08-09 09:26:21 UTC"},{"authoremail":"robbat2@gentoo.org","authorname":"Robin H. Johnson","body":"This commit represents a new era for Gentoo:\nStoring the gentoo-x86 tree in Git, as converted from CVS.\n\nThis commit is the start of the NEW history.\nAny historical data is intended to be grafted onto this point.\n\nCreation process:\n1. Take final CVS checkout snapshot\n2. Remove ALL ChangeLog* files\n3. Transform all Manifests to thin\n4. Remove empty Manifests\n5. Convert all stale $Header$\/$Id$ CVS keywords to non-expanded Git $Id$\n5.1. Do not touch files with -kb\/-ko keyword flags.\n\nSigned-off-by: Robin H. Johnson \nX-Thanks: Alec Warner - did the GSoC 2006 migration tests\nX-Thanks: Robin H. Johnson - infra guy, herding this project\nX-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration\nX-Thanks: Brian Harring - wrote much python to improve cvs2svn\nX-Thanks: Rich Freeman - validation scripts\nX-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration\nX-Thanks: Michał Górny - scripts, QA, nagging\nX-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed","commitid":"56bd759df1d0c750a065b8c845e93d5dfa6b549d","committime":"2015-08-08T20:49:04","packageid":46128,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":46128,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":396,"description":"Virtual for Message Passing Interface (MPI) v2.0 implementation","ebuildids":[807704],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101}],"depending":[{"block":true,"categoryid":354,"description":"Cloth patternmaking software","ebuildids":[876940,876940],"firstseen":"2016-02-19T14:41:30.162172","maintainer":"fordfrog@gentoo.org","maintainername":"Miroslav Šulc","name":"valentina","packageid":65034}],"ebuilds":[{"archs":["~amd64","~ppc","~x86"],"ebuildid":807704,"firstseen":"2023-12-02T05:22:49.631514","license":"GPL-2","moddate":"2026-03-22T20:20:57","packageid":46128,"repoid":1,"slot":"0","uses":["mpi"],"version":"5.2-r1"}],"masks":[],"package":{"categoryid":353,"description":"Maximum likelihood analysis for nucleotide, amino acid, and two-state data","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"tree-puzzle","packageid":46128,"summary":"TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set."},"rdependencies":[{"block":false,"categoryid":396,"description":"Virtual for Message Passing Interface (MPI) v2.0 implementation","ebuildids":[807704],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101}],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["http:\/\/www.tree-puzzle.de"],"uses":[{"description":"Add MPI (Message Passing Interface) layer to the apps that support it","isdefault":false,"use":"mpi"}]}