Dendroscope pipeline

Dendroscope specifications

Information


Unique identifier OMICS_04266
Name Dendroscope
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Some phylogenetic trees and networks.
Input format Newick,Nexus
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 3.5.9
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Dendroscope

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Maintainer


  • person_outline Daniel H. Huson <>

Publications for Dendroscope

Dendroscope IN pipelines

 (9)
2018
PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] interval of each parameter were estimated. sumt command is used to build a consensus tree from remaining 75% of sampled trees using 50% majority rule. phylogenetic trees were viewed using dendroscope 3 program[38]., gene structure display server (gsds)[39] (http://gsds.cbi.pku.edu.cn/) is used to analyze gene structure. representative gene sequences of each phyla of animal kingdom […]

2014
PMCID: 3907288
PMID: 24499935
DOI: 10.1371/journal.pcbi.1003452

[…] for the deep branches of tols, we ran bootstrap (bs) analysis with 1,000 replicates. character state changes were recorded by specifying the ‘chglist’ option in paup*. trees were visualized using dendroscope ver. 3.0.14b [49]., to determine congruence between abundance and occurrence trees, we used the nodal module implemented in the topd/fmts package ver. 3.3 [50]. the module takes as input […]

2014
PMCID: 3991678
PMID: 24748046
DOI: 10.1371/journal.pone.0095118

[…] program in genetyx. phylogenetic analysis of amino acid sequences was also carried out using the clustalw program available at ddbj (http://www.ddbj.nig.ac.jp/). a phylogenetic tree was built using dendroscope. tm domains of the ppklrs were predicted using the sosui program (http://bp.nuap.nagoya-u.ac.jp/sosui/)., y190 strain yeast was grown on ypd medium [10 g/l yeast extract (nakalai tesque, […]

2013
PMCID: 3630128
PMID: 23637983
DOI: 10.1371/journal.pone.0062136

[…] aligned sequences are given in sheet 2 of file s1 and sheet 3 of file s2. from the final alignments neighbor-joining (nj) trees were generated using clustalx [47]. the nj trees were visualized using dendroscope [49] or loft [50] and were rooted using the latter program. the multiple sequence alignments and corresponding neighbor joining trees can be found in raw format in the ‘alignment’ […]

2012
PMCID: 3280880
PMID: 22249449
DOI: 10.1084/jem.20111980

[…] aligned with clustalw 2.0.12 multiple sequence alignment tool (larkin et al., 2007; goujon et al., 2010). based on the alignment, phylogenetic trees were calculated with clustalw2 and displayed with dendroscope 2.7.4 (huson et al., 2007)., cdr3 sequences were sorted by frequency, and sequences with the same frequency were grouped into ranks ranging from single sequences with rank 1 and high […]

Dendroscope institution(s)
Center for Bioinformatics (ZBIT), University of Tubingen, Germany; Department of Computer Science at the University of Auckland, New Zealand
Dendroscope funding source(s)
This work was partially supported by the ANCESTROME project the French National Research Agency (ANR)-10-IABI-0-01.

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