title: OrthoFocus: program for identification of orthologs in multiple genomes in family-focused studies.
abstract: The identification of orthologs to a set of known genes is often the starting point for evolutionary studies focused on gene families of interest. To date, the existing orthology detection tools (COG, InParanoid, OrthoMCL, etc.) are aimed at genome-wide ortholog identification and lack flexibility for the purposes of case studies. We developed a program OrthoFocus, which employs an extended reciprocal best hit approach to quickly search for orthologs in a pair of genomes. A group of paralogs from the input genome is used as the start for the forward search and the criterion for the reverse search, which allows handling many-to-one and many-to-many relationships. By pairwise comparison of genomes with the input species genome, OrthoFocus enables quick identification of orthologs in multiple genomes and generates a multiple alignment of orthologs so that it can further be used in phylogenetic analysis. The program is available at http://www.lipidomics.ru/.
authors.affiliation: Department of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia. ivliev.alexa@gmail.com
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Ivliev
authors.forename: Marina G
authors.initials: MG
authors.lastname: Sergeeva