Commands to run inparanoid analysis of the transcriptome of two genomes against one another. This is primarily to identify inparalogs within genomes and orthologs between two genomes. This also outputs genes that are not present in the other genome. This will probably include false positives due to genes appearing on contig break points, this has been partially ammended by removing genes that don't both a start and a stop codon. Their potential otholog in the opposing genome will not be marked however, and will therefore be a false positive in the results.