Making automated multiple alignments of very large numbers of protein sequences

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

(2012) Ari Löytynoja et al.   BIOINFORMATICS

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

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

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

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

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

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

(2011) Julie D. Thompson et al.   PLoS One

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

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

(2010) Y. Liu et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A Complete Analysis of HA and NA Genes of Influenza A Viruses

(2010) Weifeng Shi et al.   PLoS One

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

(2009) Carsten Kemena et al.   BIOINFORMATICS

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

(2009) K. Liu et al.   SCIENCE

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

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

(2008) A. Loytynoja et al.   SCIENCE