Affiliations: Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia | Novosibirsk State University, Novosibirsk, Russia
Note:  Corresponding author: Konstantin V. Gunbin, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave., 10, Novosibirsk, Russia. Tel.: +7 383 363 4923; Fax: +7 383 333 1278; E-mail: [email protected]
Abstract: SAMEM (System for Analysis of Molecular Evolution Modes), a web-based pipeline system for inferring modes of molecular evolution in genes and proteins (http://pixie.bionet.nsc.ru/samem/), is presented. Pipeline 1 performs analyses of protein-coding gene evolution; pipeline 2 performs analyses of protein evolution; pipeline 3 prepares datasets of genes and/or proteins, performs their primary analysis, and builds BLOSUM matrices; pipeline 4 checks if these genes really are protein-coding. Pipeline 1 has an all-new feature, which allows the user to obtain KR/KC estimates using several different methods. An important feature of pipeline 2 is an original method for analyzing the rates of amino acid substitutions at the branches of a phylogenetic tree. The method is based on Markov modeling and a non-parametric permutation test, which compares expected and observed frequencies of amino acid substitutions, and infers the modes of molecular evolution at deep inner branches.