W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference

(2015) Olga Chernomor et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

(2012) Julien Soubrier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes

(2011) Maria Anisimova et al.   SYSTEMATIC BIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY