{"bugs":[],"categories":[{"categoryid":393,"name":"dev-libs","summary":"The dev-libs category contains various miscellaneous programming libraries."},{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":318,"name":"sci-libs","summary":"The sci-libs category contains various science-related libraries."},{"categoryid":396,"name":"virtual","summary":"The virtual category contains packages which satisfy virtual dependencies."}],"changelog":[{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"84f5cc8e0b01513227b6bdcdb7878f3c7ac61508","committime":"2026-01-28T18:46:11","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner ","commitid":"00dbc02291a0af28a173b9b142c47639eb8abbc3","committime":"2026-01-27T23:28:12","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: drop 1.48.0"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"1627ce286dcbf4f815f966fffdc1902beaa62467","committime":"2026-01-26T23:16:07","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"12aa3d7f10b088f75d3caece450e263e1868df87","committime":"2026-01-26T23:02:20","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: Stabilize 1.48.2 amd64, #968778"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"1eaf237297aeba34c61c89509ccbacd1ce9cc9d7","committime":"2026-01-14T23:00:50","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner ","commitid":"8c557e6fa26ffeddcbd8c63727632f17e13c43da","committime":"2026-01-14T22:56:41","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: Drop back to ~amd64, update description"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Closes: https:\/\/bugs.gentoo.org\/681640\nSigned-off-by: Andreas Sturmlechner ","commitid":"1d568bfbf7494a2168ef8d652b64675afbbd76e5","committime":"2026-01-14T21:08:33","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: drop 1.27.0-r1"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Closes: https:\/\/bugs.gentoo.org\/965517\nSigned-off-by: Andreas Sturmlechner ","commitid":"ab02fb8c66c9c248f740e9b6997967153fdce4a1","committime":"2026-01-14T21:06:21","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: add 1.48.2 and fix build w\/ boost-1.89"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"fd19d21addb902ce2c60c4fc7cbc8dc61eb69fb8","committime":"2024-12-03T11:18:31","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Signed-off-by: Sam James ","commitid":"59a64e369dca3abad2ee62d2f600943613bd30f8","committime":"2024-12-03T11:14:07","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: Stabilize 1.48.0 amd64, #945569"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"4f8cbd9255897b4fff78b707dab395146aa3b614","committime":"2024-03-22T09:03:55","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Closes: https:\/\/bugs.gentoo.org\/927495\nSigned-off-by: Sam James ","commitid":"2186e8d7f1080d3b350e12f7c21d538c07fa14dd","committime":"2024-03-22T08:49:27","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: uncomment patch..."},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e061d60ca9ba626f4f230539f442195962ae7a16","committime":"2024-03-22T08:48:44","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Filter LTO too, and no-SA. Not reported upstream as it has a lot of open\nbugs already and seems low activity.\n\nCloses: https:\/\/bugs.gentoo.org\/862273\nSigned-off-by: Sam James ","commitid":"4aa71fb389486acee786f07025f7e24cfa07360a","committime":"2024-03-22T08:11:38","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: add 1.48.0"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f2979793991144637956e4225ce4d0235900c1a2","committime":"2023-06-09T15:16:56","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"arthurzam@gentoo.org","authorname":"Arthur Zamarin","body":"Signed-off-by: Arthur Zamarin ","commitid":"21f3faba1e16c17ef4c03dc6558f1c93173fe72e","committime":"2023-06-03T14:46:07","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: destabilize for ~x86"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"3a4caf812f3d4f9f854838fb0fb640311a31cc32","committime":"2021-04-05T14:34:55","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-3.0.18, Repoman-3.0.3\nSigned-off-by: David Seifert ","commitid":"17ca0e1b3b8cda81f6028b21303d8c64021c2947","committime":"2021-04-05T14:14:41","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: Port to EAPI 7"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2fbdfbc003d28cd80696303439a07a13ff2dc035","committime":"2018-05-21T17:29:55","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"m.mairkeimberger@gmail.com","authorname":"Michael Mair-Keimberger","commitid":"1eb2ddf01f1ad34b00265cf46e5a4e6b3d82b1e7","committime":"2018-05-21T10:13:08","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: use HTTPs"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":45640,"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":45640,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"4f474bfa8a4d43de92a11ab3ae451da0536dccef","committime":"2015-09-25T19:01:44","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Package-Manager: portage-2.2.21\nSigned-off-by: Justin Lecher ","commitid":"06eacdf47da231ea1e9beebcad176a8fda063afe","committime":"2015-09-25T18:40:53","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: Drop old"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"f73652f9bc764aad100866df8c87b5b7949d7c9a","committime":"2015-09-25T14:41:43","packageid":45640,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: portage-2.2.20.1\nRepoMan-Options: --include-arches=\"x86\"","commitid":"9f365a9d5634350da97913fd8a45374b24b3127d","committime":"2015-09-25T14:23:11","packageid":45640,"repoid":1,"summary":"sci-biology\/mothur: x86 stable wrt bug #556066"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":45640,"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":45640,"repoid":1,"summary":"proj\/gentoo: Initial commit"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"08e6a967afc640a2d2a881b970374144624cdac2","committime":"2015-08-03T14:32:44","packageid":45640,"repoid":1,"summary":"2015-08-03 14:32:29 UTC"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"de8f53161c1ee084ebf264c406764240c5fccc1d","committime":"2015-07-27T20:21:03","packageid":45640,"repoid":1,"summary":"2015-07-27 20:21:01 UTC"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"a637bd65b7fef8e2be4e7fc6e9097479372e0e2e","committime":"2015-06-19T16:38:33","packageid":45640,"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":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101},{"block":false,"categoryid":318,"description":"General purpose library and file format for storing scientific data","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"xarthisius@gentoo.org","maintainername":"Kacper Kowalik","name":"hdf5","packageid":42259,"summary":"HDF5 is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I\/O."},{"block":false,"categoryid":393,"description":"Boost Libraries for C++","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"boost","packageid":45155},{"block":false,"categoryid":318,"description":"The GNU Scientific Library","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"gsl","packageid":46545,"summary":"The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages. GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more."},{"block":false,"categoryid":353,"description":"Fast, accurate chimera detection","ebuildids":[887332],"firstseen":"2012-08-15T14:43:37.194721","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"uchime","packageid":59697,"summary":"UCHIME is a new algorithm for detecting chimeric sequences. It was developed in collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob Knight. Chimeras are commonly created during DNA sample amplification by PCR, especially in community sequencing experiments using single regions such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can detect chimeras using a reference database or de novo using abundance information on the assumption that chimeras are less abundant than their parents because they must have undergone fewer rounds of amplification."}],"depending":[],"ebuilds":[{"archs":["amd64","~x86"],"ebuildid":887332,"firstseen":"2026-01-14T23:12:51.129256","license":"GPL-3","moddate":"2026-03-22T20:20:57","packageid":45640,"repoid":1,"slot":"0","uses":["boost","gsl","hdf5","mpi","readline"],"version":"1.48.2"}],"masks":[],"package":{"categoryid":353,"description":"Suite of algorithms for ecological bioinformatics","firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"mothur","packageid":45640},"rdependencies":[{"block":false,"categoryid":396,"description":"Virtual for Message Passing Interface (MPI) v2.0 implementation","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cluster@gentoo.org","maintainername":"Gentoo Cluster Project","name":"mpi","packageid":42101},{"block":false,"categoryid":318,"description":"General purpose library and file format for storing scientific data","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"xarthisius@gentoo.org","maintainername":"Kacper Kowalik","name":"hdf5","packageid":42259,"summary":"HDF5 is a file format and library for storing scientific data. HDF5 was designed and implemented to address the deficiencies of HDF4.x. It has a more powerful and flexible data model, supports files larger than 2 GB, and supports parallel I\/O."},{"block":false,"categoryid":393,"description":"Boost Libraries for C++","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"cpp@gentoo.org","maintainername":"Gentoo C++ Project","name":"boost","packageid":45155},{"block":false,"categoryid":318,"description":"The GNU Scientific Library","ebuildids":[887332],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"gsl","packageid":46545,"summary":"The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing wrappers to be written for very high level languages. GSL includes data types and routines for complex numbers, vectors, matrices, basic linear algebra subroutines (BLAS), eigensystems, simulated annealing, minimization, root finding, pseudo-random numbers, least-squares fitting, fast Fourier transforms (FFT), differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more."},{"block":false,"categoryid":353,"description":"Fast, accurate chimera detection","ebuildids":[887332],"firstseen":"2012-08-15T14:43:37.194721","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"uchime","packageid":59697,"summary":"UCHIME is a new algorithm for detecting chimeric sequences. It was developed in collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob Knight. Chimeras are commonly created during DNA sample amplification by PCR, especially in community sequencing experiments using single regions such as the 16S rRNA gene in bacteria or the fungal ITS region. UCHIME can detect chimeras using a reference database or de novo using abundance information on the assumption that chimeras are less abundant than their parents because they must have undergone fewer rounds of amplification."}],"repos":[{"branch":"master","lastcommit":"09daf722ab2fdfcd52776c73efabc1635c80eaa1","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/mothur.org\/"],"uses":[{"description":"Depend on dev-libs\/boost for make.contigs to read .gz compressed files.","isdefault":false,"packageid":45640,"use":"boost"},{"description":"Use sci-libs\/gsl to support diversity estimates for estimiator.single.","isdefault":false,"packageid":45640,"use":"gsl"},{"description":"Support Biom format 2.0 for the biom.info command via sci-libs\/hdf5.","isdefault":false,"packageid":45640,"use":"hdf5"},{"description":"Add MPI (Message Passing Interface) layer to the apps that support it","isdefault":false,"use":"mpi"},{"defaultflag":true,"description":"Enable support for libreadline, a GNU line-editing library that almost everyone wants","isdefault":true,"use":"readline"}]}