QuickTree protocols

QuickTree specifications

Information


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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Maintainer


  • person_outline Kevin Howe <>

Publication for QuickTree

QuickTree IN pipelines

 (9)
2012
PMCID: 3290609
PMID: 22393364
DOI: 10.1371/journal.pone.0031540

[…] 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]., […]

2011
PMCID: 3141262
PMID: 21447561
DOI: 10.1093/nar/gkr154

[…] software r (19)., multiple sequence alignments were generated with clustalw (20), and phylogenetic trees were constructed using the neighbor-joining (nj) method implemented in the software quicktree (21). tree topology reliability was assessed with the bootstrap method using 1000 replications. treedyn (22) was used to visualize and annotate the trees. trees were annotated […]

2010
PMCID: 2853128
PMID: 20064877
DOI: 10.1093/nar/gkp1219

[…] fraction of the homologous domains identified, and tree coverage, the weighted fraction of tree partitions covered in the search. a phylogenetic tree for each query domain family was generated using quicktree [v. 1.1, ref. (20)]. the multiple sequence alignments were built with hmmer [v. 2.3.2, ref. (21)] and the pfam hmm model. tree coverage is the weighted sum of the branch lengths […]

2010
PMCID: 2996957
PMID: 20624324
DOI: 10.1186/1471-2164-11-429

[…] users have to confirm that a java runtime environment (jre) is installed on their local machine before visualizing the alignment results. once a multiple sequence alignment job is finished, the quicktree program can be directly applied to construct a phylogenetic tree using the neighbor-joining algorithm [12]. the reliability of the tree can be evaluated with the bootstrap method […]

2009
PMCID: 2680407
PMID: 19393099
DOI: 10.1186/1471-2105-10-123

[…] to use this program, a java runtime environment is needed on the local computer). to investigate the evolutionary relationship of genes or proteins stored in the workset, users can directly use the quicktree program to construct a phylogenetic tree [25], which is based on the neighbor-joining algorithm. the reliability of the tree can be evaluated with different replicates of bootstrapping […]

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

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