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Protocols

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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Documentation


Maintainer


  • person_outline Daniel H. Huson

Publications for Dendroscope

Dendroscope citations

 (481)
call_split

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
call_split See protocol

[…] ce alignment (>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

[…] sed 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). […]

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

[…] were 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 []. […]

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

[…] 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.  for […]

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

[…] rotein 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 compar […]

call_split

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
call_split See protocol

[…] the 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 RD […]

Citations

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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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