supFile-all_trees_2017-07-01

Final trees from all analyses in nexus format

Individual gene trees from UCE loci

Individual gene trees per UCE locus were generated using RAxML's GTRGAMMA model of nucleotide evolution and fast bootstrapping options (replicates=1,000). Individual trees are in Newick format

Alignments of individual UCE loci

Individual alignments of UCE loci in nexus format. Loci were aligned using MAFFT and trimmed wtih Gblocks

assembled_contigs_from_UCEenriched_reads

All loci assembled from baited reads (per taxa). These sequences were then compared in an all-vs-all manner to identify homologous UCE loci among taxa. As a results, there are some contigs that may not be present in the final alignments since they are not UCE loci