This directory contains data related to the analysis of protein-coding genes. The datasets tarball contains alignments and scripts used to produce alignments for two datasets: 1) expanded (including Moa and cormorant genomes added to alignments from OMA) 2) reduced (ratites and neognaths from the OMA homology analysis only) Species included in the reduced alignments are: Anas platyrhynchos Aptenodytes forsteri Aquila chrysaetos canadensis Calypte anna Chaetura pelagica Charadrisu vociferus Columba livia Corvus brachyrhynchos Cuculus canorus Egretta garzetta Falco peregrinus Ficedula albicollis Gallus gallus Geospiza fortis Haliaeetus leucocephalus Meleagris gallopavo Melopsittacus undulatus Nipponia nippon Picoides pubescens Pseudopodoces humilis Pygoscelis adeliae Serinus canaria Struthio camelus australis Taeniopygia gutta Tinamus guttatus Balearica regulorum Fulmarus glacialis Leptosomus discolor Mesitornis unicolor Alligator mississippiensis Anolis carolinensis Chrysemys picta Dromaius novaehollandiae Rhea americana Rhea pennata Apteryx owenii Apteryx haastii Apteryx rowi Casuarius casuarius Crypturellus cinnamomeus Nothoprocta perdicaria Eudromia elegans The expanded alignments add to this: Anomalopteryx didiformis Phalacrocorax harrisi Phalacrocorax auritus Phalacrocorax brasilianus Phalacrocorax pelagic us See readmes in the datasets subdirectory for further details about producing these input files. The results tarball contains output files for a variety of molecular evolutionary analyses: paml_M0_*.txt.gz: parsed output of the PAML M0 model with ancestral reconstruction (must and parsedmuts files provide ancestral reconstruction information, parsed model parameters). This was run only on the reduced dataset. relax_parsed_*: parsed output of the RELAX model in HyPhy, run with ratites as the foreground branch. K = K values, Pval = raw Pvalue. bsresl_*: parsed output of the aBS-REL model run in HyPhy for the expanded (extended) dataset and the reduced dataset. aa_trees*: parsed AA tree branch length estimates from PAML aaml for both the reduced and expanded datasets all_besthit.out: blastp search results for all proteins used for the OMA analysis (reduced dataset only) branch_perms: outputs from RERconverge for real data (flightless_*) and random trios of three non-ratite lineages (random_*_*) The scripts tarball contains scripts and some intermediate output files. See included readmes for details.