{"id":82,"date":"2014-09-03T08:48:21","date_gmt":"2014-09-03T08:48:21","guid":{"rendered":"http:\/\/wasabiapp.org\/loytynojalab\/?page_id=82"},"modified":"2026-10-23T09:09:54","modified_gmt":"2026-10-23T09:09:54","slug":"software","status":"publish","type":"page","link":"http:\/\/loytynojalab.biocenter.helsinki.fi\/?page_id=82","title":{"rendered":"Software"},"content":{"rendered":"<div>\n<p>Active software development projects:\u00a0<\/p>\n<ul>\n<li>Twitcher and Twitcher Workbench, analysis and annotation of template switch mutations: <a href=\"https:\/\/twitcher.it.helsinki.fi\">https:\/\/twitcher.it.helsinki.fi<\/a> \u00a0<\/li>\n<\/ul>\n<p>Some of the research software developed in the group:<\/p>\n<ul>\n<li>Wasabi, visualisation of rich MSAs and graphical interface to command-line programs: <a href=\"https:\/\/github.com\/veidenberg\/wasabi\">https:\/\/github.com\/veidenberg\/wasabi<\/a><\/li>\n<li>PRANK, phylogeny-aware alignment of DNA, codon and amino-acid sequences: <a title=\"PRANK\" href=\"https:\/\/ariloytynoja.github.io\/prank-msa\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/ariloytynoja.github.io\/prank-msa<\/a>.<\/li>\n<li>PAGAN, phylogeny-aware sequence alignment and alignment extension: <a title=\"PAGAN\" href=\"https:\/\/ariloytynoja.github.io\/pagan-msa\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/ariloytynoja.github.io\/pagan-msa<\/a>.<\/li>\n<li>FPA, alignment with template switching: <a title=\"FPA\" href=\"https:\/\/github.com\/ariloytynoja\/fpa\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/github.com\/ariloytynoja\/fpa<\/a>.<\/li>\n<li>S\u00e9ance, community analysis of 18S rRNA marker gene data: <a title=\"Seance\" href=\"https:\/\/github.com\/ariloytynoja\/seance\" target=\"_blank\" rel=\"noopener noreferrer\">https:\/\/github.com\/ariloytynoja\/seance<\/a>.<\/li>\n<li>Canopy, iterative co-estimation of tree and MSA: <a title=\"Canopy\" href=\"https:\/\/github.com\/ariloytynoja\/canopy\">https:\/\/github.com\/ariloytynoja\/canopy<\/a>.<\/li>\n<li>Legacy code for ProAlign: <a href=\"https:\/\/github.com\/ariloytynoja\/ProAlign\">https:\/\/github.com\/ariloytynoja\/ProAlign<\/a>.<\/li>\n<\/ul>\n<p><!-- \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n<p>Contact: <a href=\"mailto:ari.loytynoja-at-helsinki.fi\" rel=\"nofollow\">ari.loytynoja-at-helsinki.fi<\/a> --><\/p>\n<\/div>\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Active software development projects:\u00a0 Twitcher and Twitcher Workbench, analysis and annotation of template switch mutations: https:\/\/twitcher.it.helsinki.fi \u00a0 Some of the research software developed in the group: Wasabi, visualisation of rich MSAs and graphical interface&#46;&#46;&#46;<\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-82","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/PbLaFI-1k","_links":{"self":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/pages\/82","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=82"}],"version-history":[{"count":19,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/pages\/82\/revisions"}],"predecessor-version":[{"id":666,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/pages\/82\/revisions\/666"}],"wp:attachment":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=82"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}