publication . Article . Other literature type . 2009

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan Price;
Open Access English
  • Published: 17 Apr 2009 Journal: Molecular Biology and Evolution, volume 26, issue 7, pages 1,641-1,650 (issn: 0737-4038, eissn: 1537-1719, Copyright policy)
  • Publisher: Oxford University Press
Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, ...
free text keywords: Research Articles, minimum evolution, Neighbor-Joining, large phylogenies, k-nearest neighbors algorithm, Biology, Speedup, Pairwise comparison, Algorithm, Neighbor joining, Distance matrix, Bioinformatics, Bootstrapping, Genetics, Joins, Network topology
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publication . Article . Other literature type . 2009

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan Price;