QuickTree protocols

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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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  • person_outline Kevin Howe <>

Publication for QuickTree

QuickTree in pipelines

 (12)
2015
PMCID: 4540965
PMID: 25944916
DOI: 10.1093/molbev/msv109

[…] over 300 sites (pdb: 3utl). the alignments and trees are provided as supplementary material, supplementary material online. all phylogenetic analysis was conducted using wag + γ + i. fig. 8., quicktree () was used to compute neighbor-joining trees from alignments downloaded from the http://bioinfadmin.cs.ucl.ac.uk/downloads/psicov (last accessed may 21, 2015). a single very large data set […]

2014
PMCID: 3896382
PMID: 24465495
DOI: 10.1371/journal.pone.0085139

[…] reconstruction might be computational feasible for up to ∼100k sequences using fast msa heuristics such as mafft and efficient implementations of the canonical neighbour-joining (nj) method such as quicktree or rapidnj , or heuristics such as clearcut . for larger-scale sequence classification, machine learning based methods such as (profile) hidden markov models (hmm) and support vector […]

2014
PMCID: 3914697
PMID: 24398376
DOI: 10.1093/gbe/evu007

[…] phylogenetic analysis of all sequences matching the hmm profile. first, the complete sequence data set was aligned with clustalw-mpi () and subjected to neighbor-joining tree reconstruction with quicktree (). second, all protein sequences were clustered based on their pairwise distances (≤0.3). for each cluster, the sequence with the minimum sum of pairwise distances to other members […]

2014
PMCID: 4159009
PMID: 25062915
DOI: 10.1093/gbe/evu161

[…] of all pfama families from pfam database. multiple sequence alignment (msa) for each family was built using clustalw. for phylogenetic analysis, bootstrapped trees were built and visualized using quicktree () tool of phylip package and itol, respectively. the phylogenetic trees can be accessed using the url http://itol.embl.de/shared/shradha (last accessed july 30, 2014). also the newick […]

2012
PMCID: 3474794
PMID: 23082107
DOI: 10.1371/journal.pone.0042047

[…] blastp. full-length sequences of significant blastp hits were retrieved and then a multiple alignment was generated using muscle. from this alignment, a neighbor-joining tree was produced using quicktree to determine the phylogenetic placement of the query sequence by comparing the taxonomic classification of the sequence(s) that clade with the query. if the taxonomic information differed […]


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QuickTree in publications

 (34)
PMCID: 5732528
PMID: 29246178
DOI: 10.1186/s40168-017-0379-y

[…] alignments were done using mafft (--auto) [], which brought efficiency to the pipeline with its parallelism implementation and efficient memory utilization. then, phylogenetic trees were produced by quicktree [] using the neighbor-joining algorithm. the python package ete3 was used to draw and collapse the phylogenetic trees [] to better visualize the relationship between the mobile sulfonamide […]

PMCID: 5114598
PMID: 27834372
DOI: 10.1038/ncomms13390

[…] by their physical position order. the parameter to define a cluster was two or more r genes that occurred within a maximum of ten non-r and r genes. the neighbour joining tree was drawn using quicktree v1.1., the newly assembled contigs >200 bp in length were placed along the to1000 chromosomes using paired-end read information. reads from the nine varieties (cabbage1, cabbage2, kale, […]

PMCID: 5342780
PMID: 27713118
DOI: 10.18632/oncotarget.12416

[…] sequences were obtained from uniprot and were aligned with their orthologs using clustalw []. finally, phylogenetic trees were constructed by neighbor-joining method implemented using the software quicktree []. tree topology reliability was assessed with the bootstrap method using 1000 replications., the two protein-protein interaction networks used in this work were constructed using […]

PMCID: 5023847
PMID: 27642638
DOI: 10.1128/mSphere.00195-16

[…] the ncbi nonredundant protein sequence database using blastp with an e value cutoff of 10−20. the seed sequence and its homologs were aligned in muscle, neighbor-joining trees were constructed in quicktree () using 100 bootstrap replicates, and each tree was annotated with genbank data using bespoke python scripting (not shown). maximum-likelihood hgt phylogenies whose topology conflicted […]

PMCID: 4496815
PMID: 26159619
DOI: 10.1186/s12864-015-1712-0

[…] of ~3.6 million snps with the “phylogenetic tree” tool located under the “genome diversity” section on galaxy (http://usegalaxy.org). “phylogenetic tree” constructs a neighbor-joining tree using the quicktree program []., complete mitochondrial genome sequences were aligned with the clustalw package in bioedit 7.6 [] using the mutiple alignment feature (blosum62 matrix, gap open penalty: 15.0, […]


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

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