OrthoFinder and HaMStR analyses

Single best candidate coding regions of all flatworm transcriptomes were predicted with TransDecoder v3.0.0 (Haas et al. 2013). The resulting flatworm proteomes, together with HumRef2015, were used to identify orthologous groups with OrthoFinder v0.7.1 (Emms and Kelly 2015). We ran HaMStR version 13.2.6 (Ebersberger et al. 2009) on S. mediterranea using the following command: (hamstr -sequence_file=Smed.dd.mod -taxon=Smed -hmmset=modelorganisms_hmmer3 -refspec=DROME -central). We used a Perl script to compare the list of putative hidden orthologs from Leapfrog to the HMM outputs of HaMStR (Supplemental File 1).