Gene trees for orthologous groups from "The evolution of nitrogen fixation in cyanobacteria"

Phylogenetic trees for the orthologous groups predicted across 49 taxa of Cyanobacteria and 16 Proteobacteria by Latysheva et al. (2012, Bioinformatics 28:603-606; doi:10.1093/bioinformatics/bts008) are provided here. For the 13854 groups containing at least three protein sequences, phylogenies were reconstructed as follows. Multiple alignment of protein sequences was performed using MAFFT (Katoh and Toh 2008, doi:10.1093/bib/bbn013), in "E-INS-I" mode with 1000 iterations. A phylogenetic model was selected for each protein multiple alignment by the Bayesian Information Criterion in MODELGENERATOR (Keane et al. 2006, doi:10.1186/1471-2148-6-29), with four Gamma-distributed rate categories for "+G" models. 200 bootstrap replicates of the multiple alignment were generated using seqboot in the PHYLIP package (Felsenstein, J. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle). Using the selected model, phylogeny was reconstructed by maximum likelihood with PhyML (Guindon et al. 2010, doi:10.1093/sysbio/syq010), both for the original alignment and for the bootstrap replicates.