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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 citations

 (412)
library_books

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia

2018
PLoS One
PMCID: 5933776
PMID: 29723202
DOI: 10.1371/journal.pone.0195860

[…] (>2.8 million positions) of all included genomic sequences [], from which an approximately-maximum-likelihood phylogenetic tree was generated using fasttree v2.1.10 [] and displayed with dendroscope v3.5.9 []. because no full-length, polished genomic sequences of usa100 were available, we corroborated results by generating trees using as references concatenated contigs usa100 isolate […]

library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] on concatenated sequences for arsrbc and rmlst in accordance with the procedure described for the rmlst tree described above. both trees were compared after construction of a tanglegram by use of dendroscope software (v3.5.9; http://dendroscope.org)., the results from the susceptibility testing with antimicrobial substances and from the short-read mapping (resistance determinants) […]

library_books

Identification of two different chemosensory pathways in representatives of the genus Halomonas

2018
BMC Genomics
PMCID: 5907407
PMID: 29669514
DOI: 10.1186/s12864-018-4655-4

[…] performed with the maximum likelihood package phyml3 []. all sequences were scanned for motifs in http://www.genome.jp/tools/motif/ using prosite and pfam as databases., trees were visualized with dendroscope v3.2.10 [] and final tree editing was done using itol []., for the screening of general chemotactic behavior of h. titanicae khs3 soft agar plates were prepared with modified h1 minimal […]

library_books

Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

2018
Nat Commun
PMCID: 5899146
PMID: 29654279
DOI: 10.1038/s41467-018-03949-8

[…] that the s. sonnei sublineage 3 plasmid was present in the e. coli outbreak isolate (supplementary fig. )., comparative phylogenetics of pksr100 with whole-genome phylogenies was conducted within dendroscope. the whole-genome phylogenies were (from top to bottom): a bayesian-inferred phylogenetic tree of s. flexneri 3a based on 1243 variable sites (from ref. ); the tree presented in fig. […]

library_books

Pervasive Chimerism in the Replication Associated Proteins of Uncultured Single Stranded DNA Viruses

2018
Viruses
PMCID: 5923481
PMID: 29642587
DOI: 10.3390/v10040187

[…] sequences is essential. we used two complementary approaches to detect possible recombination in rep proteins. first, we generated a tanglegram of the rep endonuclease and helicase trees using dendroscope v3 []. sequences or sequence groups whose positions differed in both trees were marked as possible recombinants. second, to substantiate the results, we performed an all-against-all […]

library_books

Analysis of DNAs associated with coconut foliar decay disease implicates a unique single stranded DNA virus representing a new taxon

2018
Sci Rep
PMCID: 5890292
PMID: 29632309
DOI: 10.1038/s41598-018-23739-y

[…] gtr + g + i substitution model, chosen after model test in mega7. bbtv dna-r (genbank acc. no. s56276) served to root the tree, and nodes with less than 70% bootstrap support were collapsed using dendroscope, v3.5.8. the final graphics were done in figtree v1.4.3. (http://tree.bio.ed.ac.uk/software/figtree/). a recombination analysis was carried out using the recombination detection package […]


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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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