MUSCLE: multiple sequence alignment with high accuracy and high throughput

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1997 • 71,835 citations

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

1994 • 63,397 citations

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

1987 • 59,130 citations

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

2002 • 14,451 citations

The Neutral Theory of Molecular Evolution

1979 • 7,965 citations

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton

2000 • 6,765 citations

SCOP: A structural classification of proteins database for the investigation of sequences and structures

1995 • 6,372 citations

The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance

1937 • 4,113 citations

The Use of Ranks to Avoid the Assumption of Normality Implicit in the Analysis of Variance

1937 • 3,577 citations

SMART, a simple modular architecture research tool: Identification of signaling domains

1998 • 3,523 citations

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

1998 • 2,048 citations

Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

1987 • 1,899 citations

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

2001 • 1,347 citations

SMART: a web-based tool for the study of genetically mobile domains

2000 • 1,298 citations

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

2003 • 1,103 citations

On the Complexity of Multiple Sequence Alignment

1994 • 935 citations

A comprehensive comparison of multiple sequence alignment programs

1999 • 763 citations

Touring protein fold space with Dali/FSSP

1998 • 669 citations

The ASTRAL compendium for protein structure and sequence analysis

2000 • 493 citations

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.

1999 • 483 citations

T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment

2000 • 389 citations

Some biological sequence metrics

1976 • 374 citations

Recent progress in multiple sequence alignment: a survey

2002 • 358 citations

Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology

1996 • 338 citations

Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments

1996 • 331 citations

SMART: identification and annotation of domains from signalling and extracellular protein sequences

1999 • 325 citations

COMPASS: A Tool for Comparison of Multiple Protein Alignments with Assessment of Statistical Significance

2003 • 282 citations

Rose: generating sequence families.

1998 • 277 citations

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

1984 • 261 citations

Large-scale comparison of protein sequence alignment algorithms with structure alignments

2000 • 251 citations

Structure Comparison and Structure Patterns

2000 • 209 citations

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

2001 • 188 citations

NCBI Reference Sequence Project: update and current status

2003 • 175 citations

Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method

2002 • 157 citations

Local homology recognition and distance measures in linear time using compressed amino acid alphabets

2004 • 149 citations

CAFASP‐1: Critical assessment of fully automated structure prediction methods

1999 • 144 citations

A comparison of scoring functions for protein sequence profile alignment

2004 • 131 citations

Comprehensive study on iterative algorithms of multiple sequence alignment

1995 • 122 citations

The Neutral Theory of Molecular Evolution

1984 • 105 citations

CAFASP-1: Critical assessment of fully automated structure prediction methods

1999 • 105 citations

Align-m—a new algorithm for multiple alignment of highly divergent sequences

2004 • 93 citations

COACH: profile–profile alignment of protein families using hidden Markov models

2004 • 89 citations

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

2003 • 78 citations

Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins

1995 • 68 citations

Phylogenetic inference in protein superfamilies: analysis of SH2 domains.

1998 • 65 citations

MaxBench: evaluation of sequence and structure comparison methods

2002 • 10 citations