Polystomatidae_MAFFT_alignment
Description
Multiple sequence alignments of the family Polystomatidae, based on the markers 12S, 18S, 28S and cox1 and the corresponding Maximum Likelihood trees inferred with IQtree. The full_taxa_set alignment includes taxa from across Polystomatidae whereas the reduced_taxa_set alignment is restricted to taxa from the "Polbatrach" clade. These are the alignments used to construct the phylogeny of Polystomatidae in the paper "Amended diagnosis, mitochondrial genome, and phylogenetic position of Sphyranura euryceae (Neodermata, Monogenea, Polystomatidae), a parasite of the Oklahoma salamander."
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Steps to reproduce
The four sequence sets (12S, 18S, 28S and cox1) were aligned per marker using MAFFT v.7.310 and trimmed using TrimAl v.1.2 “strict mode''. Selection of trimming criteria was based upon visual inspection in AliView v.1.28. The four separate alignments were then concatenated into a single alignment using the script concat.py v.0.21 (https://github.com/reslp/concat). PartitionFinder2 was used to select the best partitioning scheme and IQtree was used to infer phylogeny.