DOI: 10.5061/dryad.gv1q5
title: Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

description: Proteins have distinct structural and functional constraints at different
 sites that lead to site-specific preferences for particular amino acid
 residues as the sequences evolve. Heterogeneity in the amino acid
 substitution process between sites is not modeled by commonly used
 empirical amino acid exchange matrices. Such model misspecification can
 lead to artefacts in phylogenetic estimation such as long-branch
 attraction. Although sophisticated site-heterogeneous mixture models have
 been developed to address this problem in both Bayesian and maximum
 likelihood (ML) frameworks, their formidable computational time and memory
 usage severely limits their use in large phylogenomic analyses. Here we
 propose a posterior mean site frequency (PMSF) method as a rapid and
 efficient approximation to full empirical profile mixture models for ML
 analysis. The PMSF approach assigns a conditional mean amino acid
 frequency profile to each site calculated based on a mixture model fitted
 to the data using a preliminary guide tree. These PMSF profiles can then
 be used for in-depth tree-searching in place of the full mixture model.
 Compared with widely used empirical mixture models with k classes, our
 implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the
 computation by approximately k /1.5-fold and requires a small fraction of
 the RAM. Furthermore, this speedup allows, for the first time, full
 nonparametric bootstrap analyses to be conducted under complex
 site-heterogeneous models on large concatenated data matrices. Our
 simulations and empirical data analyses demonstrate that PMSF can
 effectively ameliorate long-branch attraction artefacts. In some empirical
 and simulation settings PMSF provided more accurate estimates of
 phylogenies than the mixture models from which they derive.
description: simuLBA.C20F.fourtaxa.tar: 4taxa 20K sitesThe 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.simuLBA.C20F.fourtaxa.tar.gzsimuLBA.C60F.fourtaxa.tar: 4 taxa 20K sitesThe 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.simuLBA.C60F.fourtaxa.tar.gzsimuLBR.C20F.fourtaxa.tar: 4 taxa 20K sitesThe sequence data were simulated under LG+C20+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.simuLBR.C20F.fourtaxa.tar.gzsimuLBR.C60F.fourtaxa.tar: 4 taxa 20K sitesThe sequence data were simulated under LG+C60+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.simuLBR.C60F.fourtaxa.tar.gzsimuLBR.8taxa.tre.seqThe 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.simuLBR.12taxa.tre.seqThe 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.simuLBR.16taxa.tre.seqThe 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.simuLBR.20taxa.tre.seqThe 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.Supplementary Materials: main filePMSF.Sup.Materials.pdfSupplementary Materials: file 2PMSF.Sup.Materials.2.pdfsimuLBA.LGFG.tarSimulation under LG+F+G for 4 taxa 1000 sites under LBA setting.simuLBR.LGFG.tarSimulation under LG+F+G for 4 taxa 1000 sites under LBR setting.simuLBR.EXEHO.tarSimulation under EX_EHO for 4 taxa 6000 sites under LBR setting.simuLBA.EXEHO.tarSimulation under EX_EHO for 4 taxa 6000 sites under LBA setting.simu.amborella.JTT.tarSimulate under JTT+F+G based on an Amborella/Angiosperm tree for 12549 sites; used for Fig. S25.simu.Ord0245.tarBootstrap 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.simuLBA.C20F.1050sites.tarSimulation under LG+C20+F+G for 4 taxa 1050 sites under LBA setting.simuLBR.C20F.1050sites.tarSimulation under LG+C20+F+G for 4 taxa 1050 sites under LBR setting.