TreeGraph protocols

TreeGraph specifications

Information


Unique identifier OMICS_04253
Name TreeGraph
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Kai F. Müller <>

Publications for TreeGraph

TreeGraph IN pipelines

 (7)
2018
PMCID: 5871936
PMID: 29385718
DOI: 10.3390/life8010004

[…] likelihood criterion, using raxml 8.1.3 with 50 distinct randomized mp trees and 100 bootstrap resamplings under the lg+gamma model of sequence evolution [25]. phylogenetic trees were edited with treegraph [26] and affinity designer version 1.6 (https://affinity.serif.com). , to examine genome-wide chromatin interaction frequencies, hi-c maps were visualized using juicebox [27], a software […]

2017
PMCID: 5518176
PMID: 28744371
DOI: 10.1093/ve/vex017

[…] et al. 2015) with gtr + i+g4 substitution model selected using modelfinder (kalyaanamoorthy et al. 2017). branches with <60% bootstrap support (1,000 bootstrap iterations) were collapsed using treegraph2 (stover and muller 2010)., evidence of recombination in the anelloviruses identified in this study was determined using rdp 4.58 (martin et al. 2015) with default settings. sequences […]

2017
PMCID: 5684056
PMID: 29134290
DOI: 10.1186/s40529-017-0202-x

[…] branches, the bootstrap method (felsenstein 1985) was used with 1000 replicates, and groups were retained when bootstrap percentages ≥ 70. the trees obtained in these analyses were drawn with the treegraph 2 software (stover and muller 2010)., pollen from net house grown plants were harvested and analyzed by sem. pollens were fixed, dehydrated, dried in a critical point dryer (hcp-2, hitachi, […]

2015
PMCID: 4359502
PMID: 25887946
DOI: 10.1186/s12864-015-1350-6

[…] from all genomes were used to construct a neighbor joining phylogenetic tree. both core genome tree and 16s ribosomal rna tree were constructed using mega6 with 1000 bootstrapping replications [43]. treegraph 2 was used to format trees [44]., protein functions were predicted by using rpsblast program against cog database of prokaryotic proteins and metabolic pathways were predicted by blast […]

2015
PMCID: 4482086
PMID: 25883135
DOI: 10.1093/nar/gkv337

[…] (27) and clustalomega (28). neighbour-joining phylogenetic analysis and protein identity/similarity matrices were generated from multiple alignments using mega5 (29) and matgat (30), respectively. treegraph2 (31) and ugene (32) were routinely used for phylogenetic tree annotation and genome browsing, respectively. logo consensus sequences were generated using weblogo (33). the gene content […]

TreeGraph institution(s)
Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany

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