QuickTree: building huge Neighbour-Joining trees of protein sequences.
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.
Howe
Kevin
K
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. klh@sanger.ac.uk
Bateman
Alex
A
Durbin
Richard
R
D000465:Algorithms; D003628:Database Management Systems; D030562:Databases, Protein; D019143:Evolution, Molecular; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D011786:Quality Control; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D015699:HIV Envelope Protein gp120