14 research outputs found
Supplementary File S3
Subsampling and trimming strategy for phylogenetic analysi
Passerines per locus alignments gbtrimmed 80%
Per locus alignments of UCE sequences aligned with MAFFT and trimmed with Gblocks, each locus containing sequences for at least 80% of 221 taxa
Files for dating analyses in BEAST, MCMCTree
Files for dating analyses in BEAST (BEAUTI files and nucleotide data sets) and MCMCTree (control files and calibrated tree file
Passerines per locus alignments untrimmed and unfiltered
Per locus alignments of UCE sequences, no Gblocks trimming, no minimum number of taxa per locu
RAxML gene trees
Newick file of gene trees estimated using RAxM
Concatenated alignment
Concatenated alignment of 4,060 UCE loci for 221 individuals in nexus format. Charset definition of each UCE locus included. Each UCE locus aligned with MAFFT, trimmed with Gblocks and contains sequence data for at least 80% of individuals
Supplementary File S1
Sampling and sequence data characteristic
Diversification analysis files
Files used in diversification analyses in Revbayes and BAMM, including Revbayes and R scripts and summary of parameter estimates in Revbaye