fish-500-loci-enrichment-probes.fasta.gz

Fasta file of 120 BP probe sequences commercially synthesized to target UCE loci in ray-finned-fishes

fish-phylip-files-for-cloudforest-with-pol_sen-and-aci_ful.tar.gz

PHYLIP-formatted alignment file for use with CLOUDFOREST. Polypterus senegalus and Acipenser fulvescens are present in all alignements. Alignment matrices may be incomplete for other taxa

fish-probe-matches-to-uce-contigs.sqlite.gz

SQLITE database of LASTZ matches (from fish-lastz-probe-matches-to-uce-contigs.tar.gz) between assembled contigs in fish-contigs-from-uce-enrichments.tar.gz and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment

fish-probe-matches-to-genome-enabled.sqlite.gz

SQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment

fish-genetree-results-from-cloudforest.tre.gz

Gene trees generated by CLOUDFOREST

fish-computer-code-README.txt

README file providing details about computer code used as part of this research project

fish-lastz-probe-matches-to-genome-enabled.tar.gz

LASTZ matches of probes to data from genome-enabled fishes

fish-nexus-files-with-gaps-from-uce-alignment.tar.gz

NEXUS alignment files for all taxa across UCE loci, having entries for taxa with missing data

fish-nexus-file-for-mrbayes.nexus.gz

NEXUS-formatted alignment file for use with MRBAYES

fish-lastz-probe-matches-to-uce-contigs.tar.gz

LASTZ matches of probes to species-specific contigs in fish-contigs-from-uce-enrichments.tar.g