QuickTree pipeline

QuickTree specifications


Unique identifier OMICS_24969
Name QuickTree
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Either a multiple sequence alignment or a distance matrix.
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes



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  • person_outline Kevin Howe <>

Publication for QuickTree

QuickTree citations

PMCID: 3290609

[…] a local mysql database. to perform the online phylogenetic analysis of cr genes, mafft 6.717 [39] was used to generate multiple sequence alignment. the neighbor-joining (nj) method, implemented by quicktree [40], was used to generate phylogenetic result due to its good balance between accuracy and efficiency. then, phyloxml were implemented for online phylogenetic tree visualization [37]., […]

PMCID: 3235092

[…] gap distance: 5; no end gap penalty; no iteration; numiter: 1; clustering method: neighbour-joining). the alignment file was used to generate a tree file with the neighbour-joining method using the quicktree program v1.1 [36]. based on this tree file, an unrooted tree diagram was plotted with the phylip 3.67 drawtree software [37] (http://mobyle.pasteur.fr)., the full-length cgace cdna […]

PMCID: 2394772

[…] them to the profile by using hmmalign in the hmmer package. after eliminating insertions not aligned to the profiles, we carried out hierarchical clustering of the domain sequences with upgma using quicktree [60], which computes a distance matrix with the method used in clustal w [61]., domains can be classified by hierarchical clustering based on sequence similarity. however, it is impossible […]

QuickTree institution(s)
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, UK

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