ALIGNED_ALL_ORTHOLOGS.tar

ALIGNED_ALL_ORTHOLOGS folder: We used OrthoMCL to cluster ORF-centroids from all species into putative orthologs from all the species included in this study. This folder contains the putative ortholog amino acid alignments and corresponding nucleotide alignments for which there were two or more species present in the ortholog clustered by OrthoMCL (104,235 total alignments). These are available as separate files for each ortholog (104,235 total orthologs with two or more species). Amino acid and nucleotides are given in their respective folders.

- Also included is an ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta file). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analyzed for the paper).