Dendroscope statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Dendroscope

Tool usage distribution map

This map represents all the scientific publications referring to Dendroscope per scientific context
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Associated diseases

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Dendroscope specifications


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




No version available



  • person_outline Daniel H. Huson

Publications for Dendroscope

Dendroscope citations


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

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 […]


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

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; […]


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

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 using PROSITE and PFAM as databases.Trees were visualized with Dendroscope v3.2.10 [] and final tree editing was done using iTOL []. […]


Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species

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 […]


Pervasive Chimerism in the Replication Associated Proteins of Uncultured Single Stranded DNA 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 […]


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

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. ( A recombination analysis was carried out using the recombination detection package RD […]

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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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