Alignment Errors Strongly Impact Likelihood-Based Tests for Comparing Topologies

Measuring guide-tree dependency of inferred gaps in progressive aligners

(2013) Salvador Capella-Gutiérrez et al.   BIOINFORMATICS

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

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

Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae

(2013) Annamária Tóth et al.   PLoS One

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

(2010) O. Penn et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation

(2009) Li-San Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Characterization of pairwise and multiple sequence alignment errors

(2008) Giddy Landan et al.   GENE