ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium

(2019) Jacob L. Steenwyk et al.   mBio

Challenges and recommendations to improve the installability and archival stability of omics computational tools

(2019) Serghei Mangul et al.   PLOS BIOLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

(2016) Xing-Xing Shen et al.   Genome Biology and Evolution

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

(2016) Xing-Xing Shen et al.   G3-Genes Genomes Genetics

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Noisy: Identification of problematic columns in multiple sequence alignments

(2008) Andreas WM Dress et al.   Algorithms for Molecular Biology