QuickTree: building huge Neighbour-Joining trees of protein sequences

Kevin Howe; Alex Bateman; Richard Durbin

doi:10.1093/bioinformatics/18.11.1546

QuickTree: building huge Neighbour-Joining trees of protein sequences

Bioinformatics. 2002 Nov;18(11):1546-7. doi: 10.1093/bioinformatics/18.11.1546.

Authors

Kevin Howe¹, Alex Bateman, Richard Durbin

Affiliation

¹ The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. [email protected]

PMID: 12424131
DOI: 10.1093/bioinformatics/18.11.1546

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.

Publication types

Comparative Study
Evaluation Study

MeSH terms

Algorithms*
Database Management Systems*
Databases, Protein*
Evolution, Molecular
HIV Envelope Protein gp120 / genetics
Humans
Phylogeny*
Quality Control
Sensitivity and Specificity
Sequence Alignment / methods
Sequence Analysis, Protein / methods*
Software

Substances

HIV Envelope Protein gp120