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Literature DB >> 12424131

QuickTree: building huge Neighbour-Joining trees of protein sequences.

Kevin Howe¹, Alex Bateman, Richard Durbin.

Abstract

We have written a fast implementation of the popular Neighbor-Joining tree building algorithm. QuickTree allows the reconstruction of phylogenies for very large protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein sequences) that would be infeasible using other popular methods.

Entities: Gene

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Year: 2002 PMID： 12424131 DOI： 10.1093/bioinformatics/18.11.1546

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

120 in total

1. Multiple sequence alignment with the Clustal series of programs.

Authors: Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J Gibson; Desmond G Higgins; Julie D Thompson
Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971

2. A stochastic evolutionary model for protein structure alignment and phylogeny.

Authors: Christopher J Challis; Scott C Schmidler
Journal: Mol Biol Evol Date: 2012-06-21 Impact factor: 16.240

3. A novel DNA-binding motif, hallmark of a new family of plant transcription factors.

Authors: José L Carrasco; Gema Ancillo; María José Castelló; Pablo Vera
Journal: Plant Physiol Date: 2005-02 Impact factor: 8.340

4. Microbial diversity in the deep sea and the underexplored "rare biosphere".

Authors: Mitchell L Sogin; Hilary G Morrison; Julie A Huber; David Mark Welch; Susan M Huse; Phillip R Neal; Jesus M Arrieta; Gerhard J Herndl
Journal: Proc Natl Acad Sci U S A Date: 2006-07-31 Impact factor: 11.205

5. Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

Authors: Jason Evans; Luke Sheneman; James Foster
Journal: J Mol Evol Date: 2006-04-28 Impact factor: 2.395

6. Revealing the hidden functional diversity of an enzyme family.

Authors: Karine Bastard; Adam Alexander Thil Smith; Carine Vergne-Vaxelaire; Alain Perret; Anne Zaparucha; Raquel De Melo-Minardi; Aline Mariage; Magali Boutard; Adrien Debard; Christophe Lechaplais; Christine Pelle; Virginie Pellouin; Nadia Perchat; Jean-Louis Petit; Annett Kreimeyer; Claudine Medigue; Jean Weissenbach; François Artiguenave; Véronique De Berardinis; David Vallenet; Marcel Salanoubat
Journal: Nat Chem Biol Date: 2013-11-17 Impact factor: 15.040

QuickTree: building huge Neighbour-Joining trees of protein sequences.

1. Multiple sequence alignment with the Clustal series of programs.

2. A stochastic evolutionary model for protein structure alignment and phylogeny.

3. A novel DNA-binding motif, hallmark of a new family of plant transcription factors.

4. Microbial diversity in the deep sea and the underexplored "rare biosphere".

5. Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

6. Revealing the hidden functional diversity of an enzyme family.

7. The copper regulon of the human fungal pathogen Cryptococcus neoformans H99.

8. Evolution of the Ras-like small GTPases and their regulators.

9. The genomic rate of molecular adaptation of the human influenza A virus.

10. ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.