Datasets used in "Fast and accurate methods for phylogenomic analyses" and in "Naive Binning Improves Phylogenomic Analyses"

Datasets used in "Fast and accurate methods for phylogenomic analyses"

17-taxon ILS: 

500 replicates, at 8 and 32 genes: 17-taxon.tar.bz2: 

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

Please cite

• Yun Yu, Tandy Warnow, and Luay Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference, Proc. RECOMB 2011.

• Yun Yu, Tandy Warnow, and Luay Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles. J Comp Biol, 18(11): 1543-1559.

100-taxon ILS: 

10 replicates, 25 genes: 100-taxon-ILS.tar.bz2

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

• Please cite Jimmy Yang and Tandy Warnow, Fast and accurate methods for phylogenomic analyses, BMC Bioinf 2011 12 (Suppl 9:S4).

100-taxon nonILS:

 6 model conditions, 10 replicates, 25 and 50 genes

• 100L2-nonILS.tar.bz2 

• 100L3-nonILS.tar.bz2

•  100S2-nonILS.tar.bz2 

• 100L2-vbr1-nonILS.tar.bz2

•  100L2-vbr1-nonILS.tar.bz2 

• 100S2-vbr1-nonILS.tar.bz2

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

• Please cite Jimmy Yang and Tandy Warnow, Fast and accurate methods for phylogenomic analyses, BMC Bioinf 2011 12 (Suppl 9:S4).

500-taxon nonILS:

 6 model conditions, 10 replicates, 25 and 50 genes

• 500L5-nonILS.tar.bz2 

• 500S3-nonILS.tar.bz2

• 500M3-nonILS.tar.bz2

• 500L5-vbr1-nonILS.tar.bz2

• 500S3-vbr1-nonILS.tar.bz2

• 500M3-vbr1-nonILS.tar.bz2

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

• Please cite Jimmy Yang and Tandy Warnow, Fast and accurate methods for phylogenomic analyses, BMC Bioinf 2011 12 (Suppl 9:S4).

Datasets for "Naive Binning Improves Phylogenomic Analyses"

Md. Shamsuzzoha Bayzid and Tandy Warnow, Bioinformatics (to appear)

• In addition to the 17-taxon datasets listed above, this paper also studied the following data:

11-taxon ILS:

11-taxon_Bioinformatics.zip

100 replicates, 100 genes

File contents:

• species tree: 11-taxon_Bioinformatics/model_tree - the model species tree.

• gene tree (strongILS): 11-taxon_Bioinformatics/simTree_11taxa_100genes_noHGT_strongILS/simtrees_X.nex - where X is the replicate number. Each file contains 100 true gene trees.

• gene tree (weakILS): 11-taxon_Bioinformatics/simTree_11taxa_100genes_noHGT_weakILS/simtrees_X.nex - where X is the replicate number. Each file contains 100 true gene trees.

• gene alignment (strongILS): 11-taxon_Bioinformatics/modi_simSeq_strongILS/modi_sequence_X.nex - where X is the replicate number. Each file contains 100 gene sequence alignments.

• gene alignment (strongILS): 11-taxon_Bioinformatics/modi_simSeq_weakILS/modi_sequence_X.nex - where X is the replicate number. Each file contains 100 gene sequence alignments.

• Estimated gene tree (strongILS): 11-taxon_Bioinformatics/estimated_genetrees_strongILS/RepX.raxml - where X is the replicate number. Each file contains 100 estimated gene trees.

• Estimated gene tree (weakILS): 11-taxon_Bioinformatics/estimated_genetrees_weakILS/RepX.raxml - where X is the replicate number. Each file contains 100 estimated gene trees.

• Please cite Y. Chung and C. Ane (2011). Comparing two Bayesian methods for gene tree/ species tree reconstruction: a simulation with incomplete lineage sorting and horizontal gene transfer. Syst Biol 60(3): 261-275.

17-taxon ILS (estimated gene trees): 

17-taxon_Bioinformatics.zip

100 replicates, at 8 and 32 genes

File contents:

• Estimated gene trees (8-gene): 17-taxon_Bioinformatics/estimated_genetrees_8-gene/RepX.raxml - where X is the replicate number.

• Estimated gene trees (32-gene): 17-taxon_Bioinformatics/estimated_genetrees_32-gene/RepX.raxml - where X is the replicate number.