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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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Versioning


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Maintainer


  • person_outline Kevin Howe

Publication for QuickTree

QuickTree citations

 (65)
call_split

Discovery of the fourth mobile sulfonamide resistance gene

2017
Microbiome
PMCID: 5732528
PMID: 29246178
DOI: 10.1186/s40168-017-0379-y
call_split See protocol

[…] 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 r […]

library_books

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

2017
Nucleic Acids Res
PMCID: 5753285
PMID: 29145643
DOI: 10.1093/nar/gkx1134

[…] from the peptidase/inhibitor units of the homologues found. An alignment is made from the sequence library using MUSCLE () and a phylogenetic tree is made from the alignment using the UPGMA method of QuickTree (). From examining the phylogenetic tree, sequences that cluster around a holotype sequence are assigned the same MEROPS identifier as that of the holotype. A sequence that does not cluster […]

library_books

Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells

2017
Nucleic Acids Res
PMCID: 5716208
PMID: 29036642
DOI: 10.1093/nar/gkx841

[…] f ORF1) of L1 elements were extracted from genome. The pairwise distance matrix of L1 elements were calculated by CALC_DISTMX in USEARCH package (). The Neighbour Join tree was then constructed using QUICKTREE (). To identify the meaningful clusters in large L1 tree, we used an algorithm based on median pairwise patristic distance () to cluster L1 tree into 22 clusters, of which the median pairwis […]

call_split

BSocial: Deciphering Social Behaviors within Mixed Microbial Populations

2017
Front Microbiol
PMCID: 5442188
PMID: 28596759
DOI: 10.3389/fmicb.2017.00919
call_split See protocol

[…] within the R vegan package (Oksanen et al., ). To this end, first the 16S rDNA gene of the seven strains were aligned by ClustalW (Thompson et al., ) and a phylogenetic neighbor-joining tree built by QuickTree v1.1 (Howe et al., ). The latter was used to calculate unifrac distance (Lozupone and Knight, ) between the different consortium using FastUnifrac (Hamady et al., ) and then tested as a func […]

library_books

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

2017
PMCID: 5306136
PMID: 28261563
DOI: 10.3389/fcimb.2017.00028

[…] ng and trailing sequences not present in all sequences were trimmed. The trimmed and aligned sequences, with an alignment length of 1,425 bases and representing 20 unique sequences, were subjected to QuickTree V 1.1 (Howe et al., ) using the “-kimura” option to calculate the substitution rate. A copy of the 16S rRNA gene sequence from Porphyromonas asaccharolytica (PaDSM20707) was used as the out- […]

library_books

The pangenome of an agronomically important crop plant Brassica oleracea

2016
Nat Commun
PMCID: 5114598
PMID: 27834372
DOI: 10.1038/ncomms13390

[…] ermined 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. […]

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

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