Clustal Omega for making accurate alignments of many protein sequences

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

(2015) Gearóid Fox et al.   BIOINFORMATICS

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Fabian Sievers 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

Pfam: the protein families database

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

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

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

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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