TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

(2012) B. P. Blackburne et al.   MOLECULAR BIOLOGY AND EVOLUTION

STRIKE: evaluation of protein MSAs using a single 3D structure

(2011) Carsten Kemena et al.   BIOINFORMATICS

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling

(2011) Jaebum Kim et al.   NUCLEIC ACIDS RESEARCH

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities

(2010) Y. Liu et al.   BIOINFORMATICS

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

An Alignment Confidence Score Capturing Robustness to Guide Tree Uncertainty

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Upcoming challenges for multiple sequence alignment methods in the high-throughput era

(2009) Carsten Kemena et al.   BIOINFORMATICS

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

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl's 10th year

(2009) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2009) K. Liu et al.   SCIENCE

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

(2008) Stefanie Hartmann et al.   BMC EVOLUTIONARY BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE