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Phylogenomic datasets from "Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches"
dataset
posted on 2016-02-12, 21:31 authored by Steve LeavittSteve Leavitt, Felix Grewe, Todd Widhelm, Lucia Muggia, Brian Wray, H. Thorsten Lumbsch- 100, 1kb data matrix - svdquart+PAUP* (100_1kb_realPHY_v1_svdquart.nex): The ‘100, 1 kb loci’ dataset was comprised of 100, 1 kilobase loci selected from each of the 100 largest contigs in the R. melanophthalma reference genome assembly.
- 303 Core Eukaryotic Genes (CEGs)(303_CEG_rhizoplaca_v1.nex): 303 Core Eukaryotic Genes (CEGs) that passed filtering requirements - from the original 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG.
- 'CEGMA' matrix (FcC_smatrix.nex): The ‘CEGMA’ matrix included 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG
- 'REALPHY' dataset (polymorphisms_move.phy): The ‘RealPhy’ dataset was constructed by mapping reads from all sampled specimens to the R. melanophthalma reference assembly using RealPhy v1.12
- subset 'A' from the ‘100, 1 kb loci’ dataset (25a_1kb_realPHY_v1_BEAST.nex): 25-locus subsets from the ‘100, 1 kb loci’ dataset: loci 1-25.
- subset 'B' from the ‘100, 1 kb loci’ dataset (25b_1kb_realPHY_v1_BEAST.nex): subset 'B' from the ‘100, 1 kb loci’ dataset: loci 26-50
- subset 'C' from the ‘100, 1 kb loci’ dataset (25c_1kb_realPHY_v1_BEAST.nex): subset 'C' from the ‘100, 1 kb loci’ dataset: loci 51-75.
- subset 'D' from the ‘100, 1 kb loci’ dataset (25d_1kb_realPHY_v1_BEAST.nex): subset 'D' from the ‘100, 1 kb loci’ dataset: loci 76-100
- subset '1-50' from the ‘100, 1 kb loci’ dataset (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 1-50
- subset '51-100' from the ‘100, 1 kb loci’ dataset (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 51-100
