Genome dynamics across the evolutionary transition to endosymbiosis
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Abstract
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Alignment of protein sequences was performed with mafft using the “-auto” option and back translated to nucleotide alignments using pal2nal [53]. A phylogenetic tree was estimated using the JTTDCMut+F+I+G4 model in IQ-TREE v1.6.12 on the concatenated data of the same set of 188 orthologues protein clusters. This tree was then used to identify genes with significant evidences of relaxation or intensification of selection using the RELAX hypothesis testing framework in HyPhy package [54].
Given that amino acid sequences were back translated to nucleotide alignments, it would be worth assessing to what extent the tests of relaxed selection may be sensitive to/impacted by alternative translated alignments. That is, each amino acid sequence has multiple alternative nucleotide alignments.
I'm not certain how pal2nal works exactly, but from …
Alignment of protein sequences was performed with mafft using the “-auto” option and back translated to nucleotide alignments using pal2nal [53]. A phylogenetic tree was estimated using the JTTDCMut+F+I+G4 model in IQ-TREE v1.6.12 on the concatenated data of the same set of 188 orthologues protein clusters. This tree was then used to identify genes with significant evidences of relaxation or intensification of selection using the RELAX hypothesis testing framework in HyPhy package [54].
Given that amino acid sequences were back translated to nucleotide alignments, it would be worth assessing to what extent the tests of relaxed selection may be sensitive to/impacted by alternative translated alignments. That is, each amino acid sequence has multiple alternative nucleotide alignments.
I'm not certain how pal2nal works exactly, but from what I can tell it appears to generate a single translated alignment. Depending on how it "chooses" which alignment to generate, this could artificially inflate (or deflate) signal of relaxed or positive selection, as it may erode the very signals these tests use to fit model parameters.
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