{"bugs":[],"categories":[{"categoryid":353,"name":"sci-biology","summary":"The sci-biology category contains software that can be used in biological and related scientific environments."},{"categoryid":416,"name":"sci-chemistry","summary":"The sci-chemistry category contains software that can be used in chemistral 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":59041,"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":59041,"repoid":1,"summary":"*\/*: drop *-linux keywords"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"71bd9032701a39f032076a4206bc3beb92be5d78","committime":"2025-10-05T18:03:52","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Raise cmake_minimum_required to 3.28 (because ~ppc)\n\nCloses: https:\/\/bugs.gentoo.org\/952793\nCloses: https:\/\/bugs.gentoo.org\/954309\nSigned-off-by: Andreas Sturmlechner ","commitid":"d6d6c3462fed95fb6a2f32d3b24239ef62187a7e","committime":"2025-10-05T13:34:02","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: Fix build w\/ cmake-4, use GNUInstallDirs"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"f2979793991144637956e4225ce4d0235900c1a2","committime":"2023-06-09T15:16:56","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"arthurzam@gentoo.org","authorname":"Arthur Zamarin","body":"Signed-off-by: Arthur Zamarin ","commitid":"eb4e379c368828ebb7570872c28a0a64d32939a4","committime":"2023-06-03T14:48:07","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: destabilize for ~x86"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"e9337c03f898ff9bb130ad175872b02f788e327b","committime":"2022-03-06T16:53:29","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Closes: https:\/\/bugs.gentoo.org\/834302\nPackage-Manager: Portage-3.0.30, Repoman-3.0.3\nSigned-off-by: Andreas Sturmlechner ","commitid":"ef367b170487b064ce7cbc74d4140985a471bcf2","committime":"2022-03-06T16:38:59","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: Drop 20150914 (r0)"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"14be308bf7bcf1dc6194f463b816c0ead2dff94a","committime":"2022-03-06T09:06:55","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: Portage-3.0.30, Repoman-3.0.3\nRepoMan-Options: --include-arches=\"x86\"\nSigned-off-by: Agostino Sarubbo ","commitid":"2b0e8054e50fa2948bdb7ef737c4310b497031f3","committime":"2022-03-06T08:53:41","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: x86 stable wrt bug #834302"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: Portage-3.0.30, Repoman-3.0.3\nRepoMan-Options: --include-arches=\"ppc64\"\nSigned-off-by: Agostino Sarubbo ","commitid":"70ef12e551e6d7ff251e5d498cd3d50b80a9485e","committime":"2022-03-06T08:51:49","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: ppc64 stable wrt bug #834302"},{"authoremail":"ago@gentoo.org","authorname":"Agostino Sarubbo","body":"Package-Manager: Portage-3.0.30, Repoman-3.0.3\nRepoMan-Options: --include-arches=\"amd64\"\nSigned-off-by: Agostino Sarubbo ","commitid":"646c01198169d22c8246d93d5cab3a0018d4f0cd","committime":"2022-03-06T08:49:46","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: amd64 stable wrt bug #834302"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"76dfb7dc6f69ca1b04de7f395aae2a3b5a41aa6a","committime":"2022-02-27T23:06:48","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"sam@gentoo.org","authorname":"Sam James","body":"Bug: https:\/\/bugs.gentoo.org\/834302\nSigned-off-by: Sam James ","commitid":"1489c366aee882be497075a8e99c4218f34d6c15","committime":"2022-02-27T22:52:01","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: update EAPI 6 -> 8"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"39da18b49f0f1c5486a1cddc64d32bac28abc59b","committime":"2021-11-19T00:07:44","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"gyakovlev@gentoo.org","authorname":"Georgy Yakovlev","body":"Bug: https:\/\/bugs.gentoo.org\/823768\nSigned-off-by: Georgy Yakovlev ","commitid":"ecc7937f3bae403c3b73f11b63ce2c1f72f927cf","committime":"2021-11-18T23:44:02","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: de-stabilize for ~ppc, bug #823768"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"ed02c25644ed59910d36aed412300010699cdc3a","committime":"2018-10-26T20:44:08","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner \nPackage-Manager: Portage-2.3.51, Repoman-2.3.11","commitid":"ad0b411a126b5f942def05267959dde2caef12e6","committime":"2018-10-26T20:26:44","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: Drop old"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"599ed4322359221ede0febd78952cff657560458","committime":"2018-10-26T19:04:16","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"whissi@gentoo.org","authorname":"Thomas Deutschmann","body":"Package-Manager: Portage-2.3.51, Repoman-2.3.11\nSigned-off-by: Thomas Deutschmann ","commitid":"fb13b085ab41c98339fab0452e758fbbf34bcc44","committime":"2018-10-26T18:41:39","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: x86 stable (bug #668654)"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"cbbdf8164d3d7a09f45c1786dc4233ccd6793a50","committime":"2018-10-25T18:44:05","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"zlogene@gentoo.org","authorname":"Mikle Kolyada","body":"Signed-off-by: Mikle Kolyada \nPackage-Manager: Portage-2.3.49, Repoman-2.3.11","commitid":"37a64f0de83bf97e7bd0e842f187d785abfb8e6e","committime":"2018-10-25T18:20:36","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: amd64 stable wrt bug #668654"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"2b56c545a3af7318b2b6dd4eb2e39f0dcee7148b","committime":"2018-10-15T19:25:53","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"slyfox@gentoo.org","authorname":"Sergei Trofimovich","body":"Signed-off-by: Sergei Trofimovich \nPackage-Manager: Portage-2.3.51, Repoman-2.3.11\nRepoMan-Options: --include-arches=\"ppc ppc64\"","commitid":"61e1c60d003403fb2b05ddbbb0357101b17e6a14","committime":"2018-10-15T19:05:32","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: stable 20150914 for ppc\/ppc64, bug #668654"},{"authoremail":"repomirrorci@gentoo.org","authorname":"Repository mirror & CI","commitid":"469ff3287cf7769c660df9e7c31d7d09ec5d0ac9","committime":"2018-10-14T20:04:05","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"asturm@gentoo.org","authorname":"Andreas Sturmlechner","body":"Signed-off-by: Andreas Sturmlechner \nPackage-Manager: Portage-2.3.51, Repoman-2.3.11","commitid":"c57483ec6b4288705e780c7e023ccb9d23e73e6c","committime":"2018-10-14T19:39:43","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: EAPI-6 bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"fcbe21c224ca3632586ed471dc022518f5bc3858","committime":"2017-10-16T03:43:34","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"soap@gentoo.org","authorname":"David Seifert","body":"Package-Manager: Portage-2.3.11, Repoman-2.3.3","commitid":"d27a6ac610de662cbf1398caccee1fcd4bf5c2c5","committime":"2017-10-16T02:52:05","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: [QA] Add cmake-utils_src_prepare"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"25093d6359f778b8d1052f66ba9e26fc29ded21a","committime":"2017-02-28T20:35:29","packageid":59041,"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":59041,"repoid":1,"summary":"Drop $Id$ per council decision in bug #611234."},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"2a988d6ed9aa6769d5a0612e107231d192588fc4","committime":"2015-12-25T12:58:24","packageid":59041,"repoid":1,"summary":"Merge updates from master"},{"authoremail":"jlec@gentoo.org","authorname":"Justin Lecher","body":"Package-Manager: portage-2.2.26\nSigned-off-by: Justin Lecher ","commitid":"4b18842e8fc7e7ff91d89ef48e0adfa7faa7c1c5","committime":"2015-12-25T10:00:01","packageid":59041,"repoid":1,"summary":"sci-chemistry\/tm-align: Version Bump"},{"authoremail":"repo-qa-checks@gentoo.org","authorname":"Repository QA checks","commitid":"945f0d2a26da4f944fd06ad6a874f69d37ce1e06","committime":"2015-08-09T09:26:46","packageid":59041,"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":59041,"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":59041,"repoid":1,"summary":"2015-06-19 16:35:30 UTC"}],"dependencies":[{"block":false,"categoryid":396,"description":"Virtual for Fortran Compiler","ebuildids":[741447],"firstseen":"2011-04-15T18:23:49.887464","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"fortran","packageid":57236}],"depending":[{"block":false,"categoryid":353,"description":"A multiple sequence alignment package","ebuildids":[755480],"firstseen":"2010-05-04T00:54:45.661860","maintainer":"sci-biology@gentoo.org","maintainername":"Gentoo Biology Project","name":"t-coffee","packageid":49483,"summary":"T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. T-Coffee allows the combination of a collection of multiple\/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments."}],"ebuilds":[{"archs":["amd64","ppc64","~ppc","~x86"],"ebuildid":741447,"firstseen":"2022-02-28T18:31:39.467293","license":"tm-align","moddate":"2026-03-28T18:04:21","packageid":59041,"repoid":1,"slot":"0","uses":["custom-cflags"],"version":"20150914-r1"}],"masks":[],"package":{"categoryid":416,"description":"Quick & Accurate Structural Alignment","firstseen":"2012-03-21T20:52:40.034466","maintainer":"sci-chemistry@gentoo.org","maintainername":"Gentoo Chemistry Project","name":"tm-align","packageid":59041,"summary":"TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller 0.2 indicates that there is no similarity between two structures; a TM-score greater 0.5 means the structures share the same fold. What is the difference between TM-score and TM-align? The TM-score program is to compare two models based on their given and known residue equivalency. It is usually NOT applied to compare two proteins of different sequences. The TM-align is a structural alignment program for comparing two proteins whose sequences can be different. The TM-align will first find the best equivalent residues of two proteins based on the structure similarity and then output a TM-score. The TM-score values in both programs have the same definition."},"rdependencies":[{"block":false,"categoryid":396,"description":"Virtual for Fortran Compiler","ebuildids":[741447],"firstseen":"2011-04-15T18:23:49.887464","maintainer":"sci@gentoo.org","maintainername":"Gentoo Science Project","name":"fortran","packageid":57236}],"repos":[{"branch":"master","lastcommit":"52197549fd3431fa256b8edbafdcd3702dd0e134","name":"gentoo","path":"\/usr\/portage","repoid":1,"upstream":"origin"}],"tracked":false,"urls":["https:\/\/zhanggroup.org\/TM-align\/"],"uses":[{"description":"Build with user-specified CFLAGS (unsupported)","isdefault":false,"use":"custom-cflags"}]}