16 research outputs found
Additional file 4: Table S2. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice
v2. Cytochrome b blast validation. Best hits to GenBank entries for cytochrome b genes from assembled mitochondrial genomes. For N. mexicana, the best hit was to a closely related species, with the second best hit to N. mexicana. (XLS 38 kb
Additional file 2: of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice
Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb
Additional file 2: of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice
Whole mitochondrial exomes. Description: Alignment of the protein coding genes of each assembled mitogenome along with Akodon montensis, downloaded from GenBank. (TXT 257 kb
Additional file 3: Figure S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice
Cytochrome b phylogenetic validation. ML tree of the assembled cytochrome b sequences compared with cytochrome b sequences downloaded from GenBank. These results showed if the sequences from our data correlated with known cytb sequences. (PNG 60 kb
Additional file 1: Table S1. of Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice
Title of data: Cytochrome b GenBank information. Taxa names and accession numbers for cytochrome b genes downloaded from GenBank in Additional file 3: Figure S1. (XLS 28 kb
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
Alignments of individual UCE loci
Individual alignments of UCE loci in nexus format. Loci were aligned using MAFFT and trimmed wtih Gblocks
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
Ultra-Large-Scale Systems: The Software Challenge of the Future
Institute for Software Researc