Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals

One-to-one single copy protein-coding orthologs in 30 representative mammals (including Homo sapiens, Gorilla gorilla, Papio anubis, Aotus nancymaae, Microcebus murinus, Mus musculus, Rattus norvegicus, Castor canadensis, Cavia porcellus, Chinchilla lanigera, Marmota marmota, Oryctolagus cuniculus, Orcinus orca, Delphinapterus leucas, Capra hircus, Sus scrofa, Equus caballus, Ceratotherium simum, Canis lupus familiaris, Enhydra lutris, Odobenus rosmarus, Neomonachus schauinslandi, Rousettus aegyptiacus, Desmodus rotundus, Condylura cristata, Loxodonta africana, Trichechus manatus, Choloepus didactylus, Phascolarctos cinereus, Ornithorhynchus anatinus) were generated by OrthoFinder, an all-against-all BLASTP algorithm. In total, 5334 protein-coding sequences were generated. Further, codon-based alignments were generated using MACSE with default parameters. Poorly aligned regions and gaps were trimmed using Gblocks. Finally, 5333 alignments were generated (TTN was too long to align successfully).