QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

FAMSA: Fast and accurate multiple sequence alignment of huge protein families

(2016) Sebastian Deorowicz et al.   Scientific Reports

Instability in progressive multiple sequence alignment algorithms

(2015) Kieran Boyce et al.   Algorithms for Molecular Biology

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

(2015) Gearóid Fox et al.   BIOINFORMATICS

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

(2015) Erik S. Wright   BMC BIOINFORMATICS

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

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

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

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

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

Pfam: the protein families database

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

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Fast Statistical Alignment

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