Has anyone done tests of selection (Dn/Ds, MK etc) on phylogenomic data (specifically, target capture) for many species? The major problem is removing stop codons, since the locus alignments are based on target bait capture loci derived from transcriptomes, and so it's not possible to get in frame CDS from a reference genome. Thanks!
Even with target capture data, it is possible to perform dN/dS analyses using software packages like PAML, HyPhy, or CodeML.
I ended up preparing target capture alignments by trimming non-homologous sequence fragments, masking misaligned amino acid residues and producing codon-aware alignments using OMM_MACSE (Ranwez et al. 2021; Ranwez et al. 2011). Then I used BUSTED (Murrell et al. 2015) to test for selection on at least one site and at least on branch across all species + subsets of 'foreground' species.
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