Evaluating 18S Phylogenetic Placement Accuracy to Uncover Hidden Diversity in Non-Bilaterian Animals. Supplementary Files.

This repository includes all supplementary files described in the homonymous paper published in the Environmental DNA journal. Supplementary File 1: Python script used to compute the PCP from phylogenetic placement results. Supplementary File 2: Python script used to filter non-targeted taxa from phylogenetic placement results and identify queries confidently placed in branches of interest (e.g. early-branching metazoa, early-branching Ctenophora…). Supplementary FIle 3 --> complete_BT.nw, V4_BT.nw, V9_BT.nw, and common_BT.nw: 18S BTs enriched in non-Bilateria animals generated in this study. They include, respectively, all 18S sequences annotated as non-bilaterians in the PR2 database version 5.1.0, only sequences containing the V4 region, only sequences containing the V9 region, and sequences containing both hypervariable regions. Reference_alignment_complete_BT.fasta, Reference_alignment_V4_BT.fasta, Reference_alignment_V9_BT.fasta, Reference_alignment_common_BT.fasta: 18S reference alignments employed to infer the BTs and are necessary for ML-based phylogenetic placement. They include, respectively, all 18S sequences annotated as non-bilaterians in the PR2 database version 5.1.0, only sequences containing the V4 region, only sequences containing the V9 region, and sequences containing both hypervariable regions. branches_of_interest.rtf: text file showing the branch ID associated with all non-targeted taxa (non-Animals and Bilateria) in the provided BTs. The outgroup lists can be used to filter out queries confidently placed among non-targeted taxa using Supplementary File 2. The branch ID for several internal branches of interest is also annotated for each BT. Sequences --> full_length_sequences.fasta, V4_sequences.fasta, V9_sequences.fasta: Unaligned sequences included in the most taxon-rich tree for each studied barcode. The files include Full-length (4,408), V4 (3,167), and V9 (883) sequences, respectively. comparable_full-length_ali.fasta, comparable_V4_ali.fasta, comparable_V9_ali.fasta: Alignments of the full-length, V9, and V4 barcodes included in the common dataset (710 sequences) Annotation_Backbone_trees.tsv --> tsv file including taxonomic annotations (Phylum, Class, and Species) of each sequence included in the backbone trees.