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QuickTree: building huge Neighbour-Joining trees of protein sequences

The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
Bioinformatics (Impact Factor: 4.62). 12/2002; 18(11):1546-7. DOI: 10.1093/bioinformatics/18.11.1546
Source: PubMed

ABSTRACT 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.

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Available from: Alex Bateman, Jun 06, 2014
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    • "Multiple sequence alignment (MSA) for each family was built using ClustalW. For phylogenetic analysis, bootstrapped trees were built and visualized using QuickTree (Howe et al. 2002) tool of PHYLIP package and iTOL, respectively. The phylogenetic trees can be accessed using the URL http://itol.embl.de/shared/shradha "
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    • "Thus, we used a method to filter the potential non-targets based on the preliminary phylogenetic analysis of all sequences matching the HMM profile. Firstly, full sequence dataset were aligned by ClustalW-MPI (Li, 2003), and subjected to neighbor-joining tree reconstruction by Quick- Tree (Howe et al., 2002). Secondly, all protein sequences were clustered based on the pairwise distance (60.3). "
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    • "Thus, we filtered the potential nontargets based on a preliminary phylogenetic analysis of all sequences matching the HMM profile. First, the complete sequence data set was aligned with ClustalW- MPI (Li 2003) and subjected to neighbor-joining tree reconstruction with QuickTree (Howe et al. 2002). Second, all protein sequences were clustered based on their pairwise distances ( 0.3). "
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