AdaptSearch
A pipeline for the search of adaptive mutations and positively selected genes from RNASeq orthologs
As part of the phylogenomic analysis of marine species transcriptomes, a RNAseq data analysis program has been developed and integrated into the Galaxy environment under the name AdaptSearch v1. The purpose of this program is to search for orthologous genes between transcriptomes of closely related species in order to analyze coding sequences and identify transcripts/codons under positive selection within a predefined phylogenomic framework.
The program is divided into several modules that allow for RNAseq assembly filtration, orthologous gene search, alignment of these genes between species in the correct reading frame, production of a species tree, analysis of codon and amino acid composition biases, and the identification of genes and/or codons under positive selection within the Galaxy environment.
Credits
Didier Jollivet (Project Lead) DYDIV / Dynamics of the marine diversity - France - CNRS Sorbonne Université
Charlotte Berthelier (Current Contributor) UMR7144 / Adaptation and Diversity in the Marine Environment and ABiMS - Roscoff Marine Station - France - CNRS Sorbonne Université
Gildas Le Corguillé (Current Contributor) ABiMS - Roscoff Marine Station - France - CNRS/UPMC
Eric Fontanillas DYDIV / Dynamics of the marine diversity - France - CNRS Sorbonne Université
Julie Baffard ABiMS - Roscoff Marine Station - France - CNRS/UPMC
Misharl Monsoor ABiMS - Roscoff Marine Station - France - CNRS/UPMC
Victor Mataigne (Initial Developer) ABiMS - Roscoff Marine Station - France - CNRS/UPMC ABICE / Adaptation et Biologie des Invertébrés en Conditions Extrêmes