PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences

Bioinformatics. 2007 Feb 1;23(3):372-4. doi: 10.1093/bioinformatics/btl592. Epub 2006 Nov 21.


Motivation: To construct a multiple sequence alignment (MSA) of a large number (> approximately 10,000) of sequences, the calculation of a guide tree with a complexity of O(N2) to O(N3), where N is the number of sequences, is the most time-consuming process.

Results: To overcome this limitation, we have developed an approximate algorithm, PartTree, to construct a guide tree with an average time complexity of O(N log N). The new MSA method with the PartTree algorithm can align approximately 60,000 sequences in several minutes on a standard desktop computer. The loss of accuracy in MSA caused by this approximation was estimated to be several percent in benchmark tests using Pfam.

Availability: The present algorithm has been implemented in the MAFFT sequence alignment package (

Supplementary information: Supplementary information is available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Conserved Sequence
  • Sequence Alignment / methods*
  • Sequence Analysis / methods*