QuickTree: building huge Neighbour-Joining trees of protein sequences

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


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


  • HIV Envelope Protein gp120