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

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

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

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

Automated Design of Probes for rRNA-Targeted FluorescenceIn SituHybridization Reveals the Advantages of Using Dual Probes for Accurate Identification

(2014) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mathematical tools to optimize the design of oligonucleotide probes and primers

(2014) Daniel R. Noguera et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

(2014) Panagiotis Katsonis et al.   GENOME RESEARCH

Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction

(2014) Qiwei Li et al.   PLoS One

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

Making automated multiple alignments of very large numbers of protein sequences

(2013) Fabian Sievers et al.   BIOINFORMATICS

Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates

(2013) Erik S. Wright et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Graph-based modeling of tandem repeats improves global multiple sequence alignment

(2013) Adam M. Szalkowski et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts

(2011) Xin Deng et al.   BMC BIOINFORMATICS

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein tandem repeats - the more perfect, the less structured

(2010) Julien Jorda et al.   FEBS Journal

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Systematic analysis of short internal indels and their impact on protein folding

(2010) RyangGuk Kim et al.   BMC STRUCTURAL BIOLOGY

PROCAIN server for remote protein sequence similarity search

(2009) Y. Wang et al.   BIOINFORMATICS

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

(2009) Carsten Kemena et al.   BIOINFORMATICS

PROMALS3D: a tool for multiple protein sequence and structure alignments

(2008) Jimin Pei et al.   NUCLEIC ACIDS RESEARCH