Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix
Description:
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 inte…
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Date:
July 31, 2009
Creator:
N. Price, Morgan; S. Dehal, Paramvir & P. Arkin, Adam
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