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Treetrimmer specifications

Information


Unique identifier OMICS_26767
Name Treetrimmer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A tree file with or without statistical support values, a parameter input file and an optional reference list of OTU names with relevant taxonomic information.
Input format NEWICK
Output data A list of OTUs retained after pruning, with information on how many OTUs have been removed in each of the highly supported clades and a trimmed tree.
Operating system Unix/Linux, Mac OS
Programming languages Ruby
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline John Archibald

Publication for Treetrimmer

Treetrimmer citations

 (3)
library_books

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

2018
PLoS One
PMCID: 5874029
PMID: 29590215
DOI: 10.1371/journal.pone.0194487

[…] onas vaginalis and/or Giardia intestinalis MRO protein sequences as queries (initial e-value cutoff: 1E-10). Following preliminary phylogenetic analysis by FastTree [], redundant OTUs were reduced by TreeTrimmer [] for alignments containing > 140 sequences. If an alignment retained > 140 sequences even after the OTU trimming step, then the procedures were repeated using a blastp search with more s […]

library_books

Genome sequencing reveals metabolic and cellular interdependence in an amoeba kinetoplastid symbiosis

2017
Sci Rep
PMCID: 5601477
PMID: 28916813
DOI: 10.1038/s41598-017-11866-x

[…] see Supplementary Table ), with an E-value cut-off of 1E-15 and a query-target alignment length of 50% or more. After multiple sequence alignment and preliminary phylogenetic analysis using FastTree, TreeTrimmer was used to reduce OTU redundancy for alignments containing > 100 sequences using the criteria shown in Supplementary Table  (paralogs within the P. pemaquidensis and Perkinsela sp. genome […]

library_books

Heme pathway evolution in kinetoplastid protists

2016
BMC Evol Biol
PMCID: 4870792
PMID: 27193376
DOI: 10.1186/s12862-016-0664-6

[…] sing BMGE with a block size of 4 and the BLOSUM30 similarity matrix. Preliminary trees were generated using Fasttree [] and ‘dereplication’ was applied to robustly supported monophyletic clades using TreeTrimmer [] in order to reduce sequence redundancy. For each protein, the final set of sequences was selected manually. Proteins were re-aligned with MUSCLE, block selection was carried out using B […]

Citations

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Treetrimmer institution(s)
Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada; Centre for Comparative Genomics and Evolutionary, Bioinformatics, Dalhousie University, Halifax, NS, Canada; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Montreal, QC, Canada; McGill University and Génome Québec, Montreal, QC, Canada
Treetrimmer funding source(s)
Supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada.

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