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

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

Quality measures for protein alignment benchmarks

(2010) Robert C. Edgar   NUCLEIC ACIDS RESEARCH

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

(2010) M. R. Aniba et al.   NUCLEIC ACIDS RESEARCH

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Fast Statistical Alignment

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

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

(2008) W. Pirovano et al.   BIOINFORMATICS

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

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

(2008) A. Loytynoja et al.   SCIENCE