Data for "Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ"

This zip file "Fish_lateral_line_comparative_genomics_data" contains two folders and two text files. The data contained in them pretains to the manuscript: Siby Philip, João Paulo Machado, Emanuel Maldonado, Vítor Vasconcelos, Stephen J O’Brien, Warren E Johnson, and Agostinho Antunes. Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ. Mol Biol Evol first published online July 27, 2012 doi:10.1093/molbev/mss194 The first folder "nexus_sequence_and_tree_file" contain "nexus" format files for all the 34 genes used in the study, the GBlocks filtered alignment followed by the corresponding phylogenetic tree. This file was used to carry out the HYPHY compartmentalization analysis (see the manuscript for details). The phylogenetic trees were built using PHYML and the best fit nucleotide substitution model was found using MrAIC, which is presented in the text file "MrAIC_AICc_models.txt". The second folder contains the phylogenetic trees used for the PAML analysis of the Postduplication branches, thus there are only 15 trees as specified in the manuscript. The text files contain the MrAIC chosen best fit substitution model (file 1) and the PyCogent Ensembl query script used (file 2; this same script is available in the PyCogent cookbook). any further request for data or detailed results should be addressed to Siby Philip (sibyphilips at gmail dot com).