Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

(2016) Kazutaka Katoh et al.   BIOINFORMATICS

Usingde novoprotein structure predictions to measure the quality of very large multiple sequence alignments

(2015) Gearóid Fox et al.   BIOINFORMATICS

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks: Fig. 1.

(2015) Ge Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultra-large alignments using phylogeny-aware profiles

(2015) Nam-phuong D. Nguyen et al.   GENOME BIOLOGY

Systematic exploration of guide-tree topology effects for small protein alignments

(2014) Fabian Sievers et al.   BMC BIOINFORMATICS

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

(2014) Jia-Ming Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simple chained guide trees give high-quality protein multiple sequence alignments

(2014) K. Boyce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

FASTSP: linear time calculation of alignment accuracy

(2011) S. Mirarab et al.   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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