Dendroscope protocols

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Dendroscope statistics

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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



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  • person_outline Daniel H. Huson <>

Publications for Dendroscope

Dendroscope in pipelines

PMCID: 5823890
PMID: 29472725
DOI: 10.1038/s41467-018-03142-x

[…] was derived from the alignment using blosum62 substitution parameters and subsequently used to build a phylogenetic tree using the neighbor-joining method. the resulting tree was visualized using dendroscope and edited with the graphic tools gimp and coreldraw., aa15 protein sequences from t. domestica, d. melanogaster, t. castaneum, a. gambiae, and h. azteca were aligned using tcoffee […]

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[]., gene structure display server (gsds)[] ( is used to analyze gene structure. representative gene sequences of each phyla of animal kingdom […]

PMCID: 5296604
PMID: 28174312
DOI: 10.1128/mBio.02257-16

[…] analysis in the randomized accelerated maximum-likelihood program (raxml) () with 500 pseudoreplicates using the generalized time-reversible model, and the resulting tree was visualized in dendroscope ()., the sample from malaria research laboratories (mrl) was an anonymized dna sample previously collected by the mrl and provided under the mrl’s remit to undertake epidemiological […]

PMCID: 5374222
PMID: 28360178
DOI: 10.1128/genomeA.00023-17

[…] the taxonomy, rdp was also used to obtain 16s rrna gene sequences for close relatives and used in the creation of the phylogenetic trees (). all trees were inferred using fasttree (), visualized in dendroscope (), and can be found on figshare ( and, for the colwellia and shewanella isolates, […]

PMCID: 5422975
PMID: 28482799
DOI: 10.1186/s12864-017-3739-x

[…] of e. coli ecc-1470 as well as the antimicrobial multidrug resistance element of 1303 (amr-ssut in gi4) was compared in more detail for the bovine-associated strain panel with easyfig (v2.2.2) []., dendroscope was used to create tanglegrams between the cladograms of the bovine-associated strain panel wga phylogeny, gene content, or vf clustering trees. all figures were created either with r […]

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Dendroscope in publications

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 […]

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;, the results from the susceptibility testing with antimicrobial substances and from the short-read mapping (resistance determinants) […]

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 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 […]

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. […]

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 […]

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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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