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

Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments: Fig. 1.

(2015) Kieran Boyce et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2014) Fabian Sievers et al.   BMC BIOINFORMATICS

FreeContact: fast and free software for protein contact prediction from residue co-evolution

(2014) László Kaján et al.   BMC BIOINFORMATICS

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

Prediction of contacts from correlated sequence substitutions

(2013) William R Taylor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A new balance index for phylogenetic trees

(2012) Arnau Mir et al.   MATHEMATICAL BIOSCIENCES

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

CMView: Interactive contact map visualization and analysis

(2011) C. Vehlow et al.   BIOINFORMATICS

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

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

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Sequence embedding for fast construction of guide trees for multiple sequence alignment

(2010) Gordon Blackshields et al.   Algorithms for Molecular Biology

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH