Publications
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and s...
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individu...
The Sequence Alignment/Map format and SAMtools
Abstract Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads ...
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs ...
Fast and accurate short read alignment with Burrows–Wheeler transform
Abstract Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A...
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here...
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified con...
MUSCLE: multiple sequence alignment with high accuracy and high throughput
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting,...