1. msa
  2. Graph
Graph of msa
  • *
  • *
  • *
  • *
  • *
  • |\
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • | *
  • |/
  • *
  • *
  • | *
  • * |
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • |\
  • * |
  • * |
  • * |
  • * |
  • |\ \
  • | * |
  • |/ /
  • | *
  • | *
  • |/
  • *
  • *
  • *
  • | *
  • * |
  • * |
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • | *
  • |/
  • *
  • | *
  • * |
  • | *
  • * |
  • * |
  • * |
  • | *
  • | *
  • * |
  • | *
  • * |
  • * |
  • | *
  • |/
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • *
  • c609bc2 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:43:22 -0400;
  • 2df795c (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 10:43:22 -0400;
  • 3386878 Update NEWS by UBod <ulrich@bodenhofer.com> 2023-09-20 15:53:22 +0200;
  • 7d1cb0e Update DESCRIPTION by UBod <ulrich@bodenhofer.com> 2023-09-20 15:52:24 +0200;
  • 190359e Merge pull request <a href="#28">#28</a> from gancho-ivanov/patch-1 by UBod <ulrich@bodenhofer.com> 2023-09-20 15:51:40 +0200;
  • 1937b80 Fixes <a href="#27">#27</a> - Add -lpthread to PKG_LIBS for Linux by gancho-ivanov <77007944+gancho-ivanov@users.noreply.github.com> 2023-09-20 13:42:35 +0300;
  • 7688d05 update of msaConsensusSequence() and msaConsensusSequence() methods to account for recent change in function Biostrings::consensusMatrix(); version number bumped to 1.33.1 by UBod <ulrich@bodenhofer.com> 2023-07-11 12:35:17 +0200;
  • 9eba13e bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:39:34 -0400;
  • e7d2128 (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:39:34 -0400;
  • a0de789 added -std=c++14 to ClustalW; version number bumped to 1.31.7 by UBod <ulrich@bodenhofer.com> 2023-03-28 16:42:11 +0200;
  • 47114e9 update of ClustalW makefile to avoid problems arising from compiling ClustalW with C++ 17; version number bumped to 1.31.6 by UBod <ulrich@bodenhofer.com> 2023-03-23 16:22:56 +0100;
  • ef2e47a update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17; version number bumped to 1.31.5 by UBod <ulrich@bodenhofer.com> 2023-03-22 10:35:35 +0100;
  • e16d071 update of Muscle source code to avoid problems arising from compiling Muscle with C++ 17; version number bumped to 1.31.5 by UBod <ulrich@bodenhofer.com> 2023-03-22 10:32:33 +0100;
  • 9755209 fix in src/Muscle/subfams.cpp to avoid conflicting definitions on some Mac systems; version number bumped to 1.31.4 by UBod <ulrich@bodenhofer.com> 2023-02-22 12:11:11 +0100;
  • 242f69b Update to config.sub/config.guess in ClustalW and ClustalOmega; version number bumped to 1.31.3 by UBod <ulrich@bodenhofer.com> 2023-02-20 13:40:56 +0100;
  • 2604ebc Merge pull request <a href="#24">#24</a> from Yikun/master by UBod <ulrich@bodenhofer.com> 2023-02-20 13:25:03 +0100;
  • 5513fc0 Update ClustalOmega/ClustalW config.guess to latest by Yikun Jiang <yikunkero@gmail.com> 2023-02-14 14:26:44 +0800;
  • 5447559 msa() function changed such that it also works if the package is not attached to the workspace; version number bumped to 1.31.2 by UBod <ulrich@bodenhofer.com> 2022-12-14 07:25:02 +0100;
  • 398d017 Update of gc; version number bumped to 1.31.1 by UBod <ulrich@bodenhofer.com> 2022-12-05 12:55:56 +0100;
  • 155f119 (origin/RELEASE_3_16, RELEASE_3_16) Update of gc; version number bumped to 1.30.1 by UBod <ulrich@bodenhofer.com> 2022-12-05 12:54:23 +0100;
  • 2407cb9 Update of gc by UBod <ulrich@bodenhofer.com> 2022-12-05 12:43:12 +0100;
  • 79494b5 update of gc; version number bumped to 1.31.1 by UBod <ulrich@bodenhofer.com> 2022-12-02 12:06:59 +0100;
  • f08931e bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:11:38 -0400;
  • 9ce42ab bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:11:38 -0400;
  • d737051 Fix for lowercase sequences; version number bumped to 1.29.3 by UBod <ulrich@bodenhofer.com> 2022-09-28 13:24:00 +0200;
  • d6f4b25 fix in texshade.sty as suggested on TeXshade homepage at CTAN; version number bumped to 1.29.2 by UBod <ulrich@bodenhofer.com> 2022-06-24 19:41:17 +0200;
  • b04803a Fix to avoid compilation problems on newest Mac OS; version number bumped to 1.29.1 by UBod <ulrich@bodenhofer.com> 2022-06-02 12:03:38 +0200;
  • 3a035de bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:25:21 +0000;
  • b9511f3 (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:25:21 +0000;
  • 4be735d applied patch to allow msa to work with the new Windows UCRT toolchain; version number bumped to 1.27.2 by UBod <ulrich@bodenhofer.com> 2022-03-21 13:58:40 +0100;
  • c6a568a various fixes; version number bumped to 1.27.1 by UBodenhofer <ulrich@quomatic.ai> 2022-02-17 13:58:20 +0100;
  • 85abce7 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:20:34 +0000;
  • 2b1349d (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:20:34 +0000;
  • 9e7acaf further fixes of warnings; version number bumped to 1.25.3 by UBod <ulrich@bodenhofer.com> 2021-10-20 10:40:40 +0200;
  • a759391 removed build/ directory from repo to avoid installation problems; version number bumped to 1.25.2 by UBod <ulrich@bodenhofer.com> 2021-10-18 09:09:47 +0200;
  • a1a1906 Upgraded to GC 7.6.12 + corresponding changes in package by UBod <ulrich@bodenhofer.com> 2021-10-15 14:35:07 +0200;
  • c03f80a Upgraded to GC 7.6.12 + corresponding changes in package by UBod <ulrich@bodenhofer.com> 2021-10-15 14:20:54 +0200;
  • e177968 Upgraded to GC 7.6.12 + corresponding changes in package by UBod <ulrich@bodenhofer.com> 2021-10-15 14:17:47 +0200;
  • d236535 Upgraded to GC 7.6.12 + corresponding changes in package by UBod <ulrich@bodenhofer.com> 2021-10-15 12:54:55 +0200;
  • 58801f8 update of gc; version number bumped to 1.25.1 by UBod <ulrich@bodenhofer.com> 2021-10-14 12:09:56 +0200;
  • 08ea272 update of gc; version number bumped to 1.25.1 by UBod <ulrich@bodenhofer.com> 2021-10-14 12:09:27 +0200;
  • 4bd9e01 Merge pull request <a href="#14">#14</a> from mephistopheles78/master by UBod <ulrich@bodenhofer.com> 2021-10-14 11:50:21 +0200;
  • a3ab5bd update gc-version by mephistopheles78 <christoph.kainrath@gmx.at> 2021-07-29 14:00:31 +0200;
  • 5f2297b bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:13:32 +0000;
  • d939cac (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:13:32 +0000;
  • 7606297 updated texshade.sty; version number bumped to 1.23.1 by UBodenhofer <ulrich@quomatic.ai> 2021-04-29 14:32:02 +0200;
  • d7b257c bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:05:14 -0400;
  • 78bb238 (origin/RELEASE_3_12, RELEASE_3_12) bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 11:05:14 -0400;
  • 4a8d148 (origin/RELEASE_3_11, RELEASE_3_11) bug fixes; version number bumped to 1.20.1 by UBodenhofer <ulrich@quomatic.ai> 2020-09-01 10:26:45 +0200;
  • 6331ee3 addressed UPGMA error in msaClustalW() on Windows using R 4.0.x by UBodenhofer <ulrich@quomatic.ai> 2020-08-12 15:44:51 +0200;
  • 0ff2dd0 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:48:56 +0000;
  • d8361a7 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:48:56 +0000;
  • 179c40e bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:39:24 -0400;
  • bfbaad2 (origin/RELEASE_3_10, RELEASE_3_10) bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:09:18 -0400;
  • e487eb3 removed change history from vignette; version number bumped to 1.17.2 by UBodenhofer <ulrich@quomatic.ai> 2019-10-18 15:53:51 +0200;
  • 6d5174b Various fixes related to Windows build; version number bumped to 1.17.1 by UBodenhofer <ulrich@quomatic.ai> 2019-09-12 09:42:34 +0200;
  • 6abe9dc bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:12:41 -0400;
  • be1cf21 (origin/RELEASE_3_9, RELEASE_3_9) bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:55 -0400;
  • 8e00ed7 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:34 -0400;
  • b311929 (origin/RELEASE_3_8, RELEASE_3_8) bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:58 -0400;
  • d1609f4 replace BiocInstaller biocLite mentions with BiocManager by LiNk-NY <mramos09@gmail.com> 2018-08-30 13:52:42 -0400;
  • c635f4f added README and .gitignore by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2018-05-15 14:29:11 +0200;
  • 0dc4e75 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:41 -0400;
  • 5c9af26 (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:37 -0400;
  • 8848fc7 minor fix in ClustalW; version number bumped to 1.11.2 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2018-04-27 08:42:31 +0200;
  • 23e990d fix of custom substitution matrices in ClustalW; version number bumped to 1.11.1 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2018-04-23 13:29:24 +0200;
  • b77c792 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:54:10 -0400;
  • 0c9cc33 (origin/RELEASE_3_6, RELEASE_3_6) bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:40:51 -0400;
  • fa7c43d bump x.y.z versions to odd y after creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:50:57 +0000;
  • fd56444 (origin/RELEASE_3_5, RELEASE_3_5) Creating branch for BioC 3.5 release by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:45:44 +0000;
  • 29f2b81 bump x.y.z versions to even y prior to creation of 3_5 branch by Herve Pages <hpages@fhcrc.org> 2017-04-24 19:25:24 +0000;
  • a760f3e Fix for clang 4 on Mac OS; version number bumped to 1.7.2 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2017-04-17 19:52:29 +0000;
  • 7599588 Attempt to fix clang error on Mac OS ElCapitan; version number not bumped (not yet) by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2017-04-04 07:43:41 +0000;
  • 5ad9386 New functionality for computing consensus sequences and conservation scores; version number bumped to 1.7.1 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2017-03-31 11:35:08 +0000;
  • 6def718 bump x.y.z versions to odd 'y' after creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:10:43 +0000;
  • 6bbe0eb (origin/RELEASE_3_4, RELEASE_3_4) Creating branch for BioC 3.4 release by Herve Pages <hpages@fhcrc.org> 2016-10-17 19:00:47 +0000;
  • 2b6c62b bump x.y.z versions to even 'y' prior to creation of 3_4 branch by Herve Pages <hpages@fhcrc.org> 2016-10-17 18:45:06 +0000;
  • c0bc6e6 (origin/RELEASE_3_3, RELEASE_3_3) fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix; version number bumped to 1.4.5 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-08-09 15:12:10 +0000;
  • f2d8b3d fixes in ClustalOmega source code to ensure Windows compatibility of GCC6 compatibility fix; version number bumped to 1.5.5 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-08-09 14:50:55 +0000;
  • f4e5c2a minor fixes (see inst/NEWS); version number bumped to 1.4.4 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-07-20 13:22:51 +0000;
  • b9525fd minor fixes (see inst/NEWS); version number bumped to 1.5.4 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-07-20 13:18:53 +0000;
  • 01e68de commit of missing files by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-06-23 13:34:29 +0000;
  • bbc69d1 conversions extended + corresponding changes in documentation; version number bumped to 1.5.3 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-06-23 13:33:29 +0000;
  • d0503eb minor changes in package vignette; version number bumped to 1.4.3 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-06-23 13:32:48 +0000;
  • be18926 Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:18:19 +0000;
  • d83a50c Version bump to trigger package rebuilding now that purl()'ing issue has been correctly identified. knitr does not create purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is set, which the build system was setting. Now it's not set, so these .R files are now created. See https://github.com/yihui/knitr/issues/1212 for more. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-15 20:14:22 +0000;
  • 5655216 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:15:25 +0000;
  • 9134353 Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-11 23:05:31 +0000;
  • 9667b92 bump version after creating 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:30:44 +0000;
  • 2943fcb Creating branch for BioC 3.3 release. by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:26:31 +0000;
  • cb96c2a Bump versions prior to creation of 3.3 branch by Dan Tenenbaum <dtenenba@fhcrc.org> 2016-05-03 21:20:18 +0000;
  • 48323c5 Last-minute fix of msaPrettyPrint(); version number bumped to 1.3.7 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-05-02 09:23:23 +0000;
  • 8674fd7 Minor corrections and extensions (see inst/NEWS); version number bumped to 1.3.6 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-04-18 15:12:00 +0000;
  • 297b13a Minor changes in the way the help text is displayed by the msa() function; version number bumped to 1.3.5 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-04-10 14:57:52 +0000;
  • 531ad0c Correction of vignette by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-04-06 12:43:11 +0000;
  • faf12a4 Added a new function msaCheckNames; version number bumped to 1.3.4 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-04-06 12:24:49 +0000;
  • 277fd55 Minor corrections in one man page by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-02-25 16:49:06 +0000;
  • 489bd9e missing file added to svn control by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-02-25 15:24:31 +0000;
  • 8db2d6e added new conversion tools; version number bumped to 1.3.3 by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2016-02-25 15:23:41 +0000;
  • fd1f660 further fixes by Ulrich Bodenhofer <bodenhofer@bioinf.jku.at> 2015-12-21 10:29:13 +0000;