{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T09:25:35Z","timestamp":1781601935701,"version":"3.54.5"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA\u2019s graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.megasoftware.net\/<\/jats:p>\n               <jats:p>Contact: \u00a0s.kumar@asu.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts507","type":"journal-article","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T02:27:06Z","timestamp":1345861626000},"page":"2685-2686","source":"Crossref","is-referenced-by-count":334,"title":["MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Sudhir","family":"Kumar","sequence":"first","affiliation":[{"name":"1 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University (ASU) and 2School of Life Sciences, ASU, Tempe, AZ 85287-5301, USA and 3Department of Biology, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan"},{"name":"1 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University (ASU) and 2School of Life Sciences, ASU, Tempe, AZ 85287-5301, USA and 3Department of Biology, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glen","family":"Stecher","sequence":"additional","affiliation":[{"name":"1 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University (ASU) and 2School of Life Sciences, ASU, Tempe, AZ 85287-5301, USA and 3Department of Biology, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Peterson","sequence":"additional","affiliation":[{"name":"1 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University (ASU) and 2School of Life Sciences, ASU, Tempe, AZ 85287-5301, USA and 3Department of Biology, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Koichiro","family":"Tamura","sequence":"additional","affiliation":[{"name":"1 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University (ASU) and 2School of Life Sciences, ASU, Tempe, AZ 85287-5301, USA and 3Department of Biology, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2012,8,24]]},"reference":[{"key":"2023012513140423800_bts507-B1","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1093\/bib\/bbn017","article-title":"MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences","volume":"9","author":"Kumar","year":"2008","journal-title":"Brief Bioinform."},{"key":"2023012513140423800_bts507-B2","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed model","volume":"22","author":"Stamatakis","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012513140423800_bts507-B3","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2685\/48873861\/bioinformatics_28_20_2685.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/20\/2685\/48873861\/bioinformatics_28_20_2685.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:15:09Z","timestamp":1674674109000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/20\/2685\/207449"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,8,24]]},"references-count":3,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2012,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts507","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,10,15]]},"published":{"date-parts":[[2012,8,24]]}}}