Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

fish-500-loci-enrichment-probes.fasta.gzFasta file of 120 BP probe sequences commercially synthesized to target UCE loci in ray-finned-fishes.fish-contigs-from-uce-enrichments.tar.gzFASTA file of contigs assembled from raw reads generated by sequencing enriched libraries of several reptile species.fish-lastz-probe-matches-to-uce-contigs.tar.gzLASTZ matches of probes to species-specific contigs in fish-contigs-from-uce-enrichments.tar.gzfish-lastz-probe-matches-to-genome-enabled.tar.gzLASTZ matches of probes to data from genome-enabled fishes.fish-probe-matches-to-uce-contigs.sqlite.gzSQLITE 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.gzSQLITE 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-nexus-files-from-uce-alignment.tar.gzNEXUS alignment files for all taxa across UCE loci, lacking entries for taxa with missing data.fish-nexus-files-with-gaps-from-uce-alignment.tar.gzNEXUS alignment files for all taxa across UCE loci, having entries for taxa with missing data.fish-nexus-file-for-mrbayes.nexus.gzNEXUS-formatted alignment file for use with MRBAYES.fish-phylip-file-for-raxml.phylip.gzPHYLIP formatted alignment file for use with RAXML.fish-partitioned-phylip-file-for-raxml-partitions.txt.gzPartitions for use with RAXML.fish-partitioned-phylip-file-for-raxml.phylip.gzPartitioned PHYLIP file for use with RAXML.fish-phylip-files-for-cloudforest-with-pol_sen-and-aci_ful.tar.gzPHYLIP-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-genetree-results-from-cloudforest.tre.gzGene trees generated by CLOUDFOREST.fish-genetree-bootrep-results-from-cloudforest.tar.gzGene tree bootstrap replicates generated by CLOUDFOREST.fish-computer-code-README.txtREADME file providing details about computer code used as part of this research project.