Main content

Home

Menu

Loading wiki pages...

View
Wiki Version:
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).
OSF does not support the use of Internet Explorer. For optimal performance, please switch to another browser.
Accept
This website relies on cookies to help provide a better user experience. By clicking Accept or continuing to use the site, you agree. For more information, see our Privacy Policy and information on cookie use.
Accept
×

Start managing your projects on the OSF today.

Free and easy to use, the Open Science Framework supports the entire research lifecycle: planning, execution, reporting, archiving, and discovery.