The “cephalopod_core_ortholog_set” archive includes all of the files used to produce the custom cephalopod core ortholog set used in HaMStR to recover putative orthologs from all of the transcriptome assemblies used in this study.

cephalopoda.fas: Set of alignments of putative OGs, each including data for at least five of the seven reference taxa, used to build pHMMs in hmmbuild and hmmcalibrate.

hmm_dir: The pHMMs generated with hmmbuild and hmmcalibrate from cephalopoda.fas

Octopus-bimaculoides-proteome.fas: The predicted proteome for Octopus bimaculoides (downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/194/135/GCF_001194135.1_Octopus_bimaculoides_v2_0/GCF_001194135.1_Octopus_bimaculoides_v2_0_protein.faa.gz).