Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

Wang H, Minh BQ, Susko E, Roger AJ

Date Published: August 4, 2017

DOI: https://doi.org/10.5061/dryad.gv1q5

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Title simuLBA.C20F.fourtaxa.tar: 4taxa 20K sites
Downloaded 3 times
Description The sequence data (20K sites) were simulated under LG+C20+F+G for four-taxon trees under the LBA-inducing conditions. The tree files are also included.
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Title simuLBA.C60F.fourtaxa.tar: 4 taxa 20K sites
Downloaded 2 times
Description The sequence data (20K sites) were simulated under LG+C60+F+G for four-taxon trees under the LBA-inducing conditions. The tree files are also included.
Download simuLBA.C60F.fourtaxa.tar.gz (394.4 Mb)
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Title simuLBR.C20F.fourtaxa.tar: 4 taxa 20K sites
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Description The sequence data were simulated under LG+C20+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.
Download simuLBR.C20F.fourtaxa.tar.gz (361.1 Mb)
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Title simuLBR.C60F.fourtaxa.tar: 4 taxa 20K sites
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Description The sequence data were simulated under LG+C60+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.
Download simuLBR.C60F.fourtaxa.tar.gz (358.6 Mb)
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Title simuLBR.8taxa.tre.seq
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Description The sequence data were simulated under LG+C20+F+G for an 8-taxon tree under an LBR-inducing condition. The tree file is also included.
Download simuLBR.8taxa.tre.seq.gz (6.129 Mb)
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Title simuLBR.12taxa.tre.seq
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Description The sequence data were simulated under LG+C20+F+G for a 12-taxon tree under an LBR-inducing condition. The tree file is also included.
Download simuLBR.12taxa.tre.seq.gz (8.611 Mb)
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Title simuLBR.16taxa.tre.seq
Downloaded 3 times
Description The sequence data were simulated under LG+C20+F+G for a 16-taxon tree under an LBR-inducing condition. The tree file is also included.
Download simuLBR.16taxa.tre.seq.gz (11.09 Mb)
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Title simuLBR.20taxa.tre.seq
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Description The sequence data were simulated under LG+C20+F+G for a 20-taxon tree under an LBR-inducing condition. The tree file is also included.
Download simuLBR.20taxa.tre.seq.gz (13.56 Mb)
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Title Supplementary Materials: main file
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Download PMSF.Sup.Materials.pdf (2.070 Mb)
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Title Supplementary Materials: file 2
Downloaded 11 times
Download PMSF.Sup.Materials.2.pdf (141.9 Kb)
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Title simuLBA.LGFG.tar
Downloaded 1 time
Description Simulation under LG+F+G for 4 taxa 1000 sites under LBA setting.
Download simuLBA.LGFG.tar.gz (18.60 Mb)
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Title simuLBR.LGFG.tar
Downloaded 1 time
Description Simulation under LG+F+G for 4 taxa 1000 sites under LBR setting.
Download simuLBR.LGFG.tar.gz (18.28 Mb)
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Title simuLBR.EXEHO.tar
Downloaded 1 time
Description Simulation under EX_EHO for 4 taxa 6000 sites under LBR setting.
Download simuLBR.EXEHO.tar.gz (108.4 Mb)
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Title simuLBA.EXEHO.tar
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Description Simulation under EX_EHO for 4 taxa 6000 sites under LBA setting.
Download simuLBA.EXEHO.tar.gz (110.3 Mb)
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Title simu.amborella.JTT.tar
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Description Simulate under JTT+F+G based on an Amborella/Angiosperm tree for 12549 sites; used for Fig. S25.
Download simu.amborella.JTT.tar.gz (7.578 Mb)
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Title simu.Ord0245.tar
Downloaded 1 time
Description Bootstrap alignment files for fitting PMSF based on the ML tree estimated from Ord0245, one of the 300 proteins in the HSSP test datasets. These data were used for producing Fig. S1.
Download simu.Ord0245.tar.gz (281.1 Kb)
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Title simuLBA.C20F.1050sites.tar
Description Simulation under LG+C20+F+G for 4 taxa 1050 sites under LBA setting.
Download simuLBA.C20F.1050sites.tar.gz (18.60 Mb)
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Title simuLBR.C20F.1050sites.tar
Downloaded 2 times
Description Simulation under LG+C20+F+G for 4 taxa 1050 sites under LBR setting.
Download simuLBR.C20F.1050sites.tar.gz (18.26 Mb)
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When using this data, please cite the original publication:

Wang H, Minh BQ, Susko E, Roger AJ (2017) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syx068

Additionally, please cite the Dryad data package:

Wang H, Minh BQ, Susko E, Roger AJ (2017) Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Dryad Digital Repository. https://doi.org/10.5061/dryad.gv1q5
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