The process of evolutionary sequence analysis is hindered by both\u00a0software complexity and the multi-step nature of data integration, management\u00a0and visualisation. A common workflow will invoke numerous programs and\u00a0custom scripts, passing information in flat files that are named arbitrarily and can\u00a0be accidentally overwritten or deleted. This approach works fine for many smaller\u00a0problems, but does not scale. In practical settings, analysis is performed on data\u00a0from multiple sources, by multiple collaborators and repeated multiple times with\u00a0different program options, to integrate new data and update reference\u00a0information.<\/p>\n
Wasabi\u00a0is an open source, web\u2013based,\u00a0integrated environment for evolutionary sequence analysis. Wasabi is built around\u00a0the phylogeny-aware sequence alignment tools PRANK and PAGAN, which have\u00a0been shown to produce alignments that better represent evolutionary homology\u00a0and therefore aid downstream analysis such as inference of selection and\u00a0phylogenetic tree estimation. Wasabi\u2019s graphical interface simplifies analysis byhiding extraneous options, provides context sensitive menus and integrates with\u00a0Ensembl to easily allow inclusion of gene sequences, gene family alignments or\u00a0slices of genomic alignments into projects. Wasabi supports reproducibility by\u00a0automatically storing the results of intermediate steps and was designed with\u00a0collaboration and sharing in mind, featuring built\u2013in functions to share data\u00a0between users and publish analysis results to a wide audience.\u00a0Wasabi is available at http:\/\/wasabiapp.org<\/a>.<\/p>\n <\/p>\n","protected":false},"excerpt":{"rendered":" The process of evolutionary sequence analysis is hindered by both\u00a0software complexity and the multi-step nature of data integration, management\u00a0and visualisation. A common workflow will invoke numerous programs and\u00a0custom scripts, passing information in flat files...<\/p>\n","protected":false},"author":4,"featured_media":63,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"image","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_post_was_ever_published":false},"categories":[4],"tags":[],"class_list":["post-60","post","type-post","status-publish","format-image","has-post-thumbnail","hentry","category-research-topic","post_format-post-format-image"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pbLaFI-Y","jetpack_featured_media_url":"http:\/\/loytynojalab.biocenter.helsinki.fi\/wp-content\/uploads\/2014\/09\/wasabi_sharing.png","_links":{"self":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/posts\/60","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/types\/post"}],"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=60"}],"version-history":[{"count":1,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/posts\/60\/revisions"}],"predecessor-version":[{"id":68,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/posts\/60\/revisions\/68"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=\/wp\/v2\/media\/63"}],"wp:attachment":[{"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=60"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=60"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/loytynojalab.biocenter.helsinki.fi\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=60"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}