Alignment files for exons captured for all ten species

Alignment files for exons captured for all ten species plus the reference sequence from the Nile tilapia (Oreochromis niloticus). Each individual exon alignments was sorted into one of three categories: 'good', 'passable', or 'poor'. Only alignments in the categories 'good' and 'passable' categories were used for phylogenetic analysis.
Included are the concatenated alignments used for Bayesian (MrBayes; nexus format) and maximum likelihood (RAxML; phylip format) phylogenetic analyses and individual exon alignments (phylip format) used in RAxML bootstrap analyses that were ultimately analyzed in a species tree framework using MP-EST.