UCE data from all sources (Genomes, FrogCap, SRA, and newly sequenced samples), provided as unfiltered sequences, SuperCRUNCH-filtered sequences, trimmed alignments, and a concatenated matrix.
Folders:
- `1 - Unfiltered Sequences`: This contains all sequences mined from published genomes using PHYLUCE (UCE-sequences-Genomes.fasta), all sequences used from the FrogCap paper (UCE-sequences-FrogCap.fasta), and all the newly assembled sequences from NCBI SRA and new sequencing (UCE-sequences-Assembled.fasta). The newly assembled sequences include contigs for Velvet and aTRAM2 assemblies, meaning there are redundant seuqences present (potentially two sequences for a species for a locus).
- `2 - Filtered Sequences`: This contains all sequences in marker-specific fasta files that passed through SuperCRUNCH similarity filtering and selection steps. These are the final sequences per UCE that were used, but prior to alignment and trimming.
- `3 - Final Trimmed Alignments`: Contains final alignments for all UCEs. These have been trimmed using TrimAl with gap-threshold of 0.2, so the original sequences are not represented here.
- `4 - Concatenated Alignment`: Contains the concatenated UCE alignment used for the RAxML analysis, along with taxa-loci counts and marker partition information (not used in the analysis).