Datasets for "Fast and accurate methods for phylogenomic analyses"

J. Yang, T. Warnow, , RECOMB-CG 2011

The datasets in this collection are used to test methods for estimating species trees from gene trees and alignments, where the true gene trees can differ from the true species tree due to incomplete lineage sorting (ILS). The 17-taxon datasets were provided by Luay Nakhleh of Rice University, who simulated these datasets for an earlier study. These datasets evolve under Jukes-Cantor sequence evolution. We simulated the remaining datasets, some of which evolve under ILS. The model of sequence evolution for these datasets is Generalized Time Reversible (GTR) with gamma-distributed rates across sites.

17-taxon ILS: 500 replicates, at 8 and 32 genes

file contents:

• species tree: 17-taxon/st/RepXstree - where X is the replicate number
• gene tree: 17-taxon/Yloci/RepXgtrees - where X is the replicate number and Y is the number of gene trees
• gene sequences: 17-taxon/Yloci/seq/RepXgseqs - where X is the replicate number and Y is the number of gene trees

100-taxon ILS: 10 replicates, 25 genes

file contents:

• species tree: model_tree - the species tree
• gene tree: 100-taxon-ILS/seq/RepX.gtY.rose.tree.t - where X is the replicate number and Y is the gene
• gene alignment: 100-taxon-ILS/seq/RepX.gtY.rose.true.aln - where X is the replicate number and Y is the gene

100-taxon nonILS: 6 model conditions, 10 replicates, 25 and 50 genes

file contents (replace 100L2 with another model condition for the corresponding file):

• species tree: 100-taxon-nonILS/rose/100L2/rose.internal.model.100L2.reference_tree
• gene tree: 100-taxon-nonILS/rose/100L2/X/rose.internal.model.100L2.Y.tree.t - where X is the replicate number and Y is the gene
• gene alignment: 100-taxon-nonILS/rose/100L2/X/aln/rose.internal.model.100L2.Y.true_aln - where X is the replicate number and Y is the gene

500-taxon nonILS: 6 model conditions, 10 replicates, 25 and 50 genes

file contents (replace 500L5 with another model condition for the corresponding file):

• species tree: 500-taxon-nonILS/rose/500L5/rose.internal.model.500L5.reference_tree
• gene tree: 500-taxon-nonILS/rose/500L5/X/rose.internal.model.500L5.Y.tree.t - where X is the replicate number and Y is the gene
• gene alignment: 500-taxon-nonILS/rose/500L5/X/aln/rose.internal.model.500L5.Y.true_aln - where X is the replicate number and Y is the gene