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. 2017 Jun 21;18:310. doi: 10.1186/s12859-017-1726-5

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© The Author(s). 2017

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — OrthoReD overview. To determine the orthology of the gene of interest, gene of interest is used as a query for a BLASTP search against the dataset (step 1). The BLASTP hits are screened to generate a reduced dataset (step 2). All-v-all BLASTP is conducted on the reduced dataset (step 3) to generate pairwise similarity matrix used by MCL to separate the reduced dataset into clusters (step 4). Most likely phylogeny is reconstructed for the members within the cluster of interest (step 5) and long branches are subsequently removed from the tree (step 6). Finally, all members of the clade that share the most recent gene duplication event are returned as predicted orthologs (step 7)