TreeGraph protocols

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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

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Maintainer


  • person_outline Kai F. Müller <>

Publications for TreeGraph

TreeGraph in pipelines

 (12)
2018
PMCID: 5889549
PMID: 29625550
DOI: 10.1186/s12864-018-4606-0

[…] amino acid alignments using this evolutionary model in raxml v8 on the ucr hpcc cluster with 1000 bootstraps [–]. a collapsed tree was also constructed from the three- and four- species trees in treegraph 2 by collapsing any node with < 70% bootstrap support into a polytomy []., protein domains were investigated using multiple online programs including, interpro […]

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

[…] phylogenetic tree using iq-tree () with gtr + i+g4 substitution model selected using modelfinder (). branches with <60% bootstrap support (1,000 bootstrap iterations) were collapsed using treegraph2 ()., evidence of recombination in the anelloviruses identified in this study was determined using rdp 4.58 () with default settings. sequences were auto-masked for optimal recombination […]

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

[…] for branches, the bootstrap method (felsenstein ) 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 )., 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, […]

2016
PMCID: 5131910
PMID: 27906966
DOI: 10.1371/journal.pntd.0005159

[…] a chain length of 10,000,000 was run, sampling every 1,000. the best supported tree was obtained using the utility treeannotator and a burn-in of 1,000. the optimal tree was graphically modified in treegraph2 []., 3d biomolecule graphics were done using the viewer in geneious r8. pdb files containing atomic resolution data (core, 1sfk; envelope, 2i69; ns1, 4oie; helicase, 2qeq; mtase, 2oy0; […]

2015
PMCID: 4320630
PMID: 25555398
DOI: 10.1186/1471-2164-16-2

[…] quantified with the ratio of identical nodes performed in t-coffee []. the percentage of bootstrap and the posterior probability index were joined in the maximum likelihood tree using the program treegraph2 []., to determine if hgt candidates were the result of contamination a blastp (v2.2.29+) (vs the nr database of ncbi) search of the upstream and downstream protein of each candidate […]


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TreeGraph in publications

 (75)
PMCID: 5889549
PMID: 29625550
DOI: 10.1186/s12864-018-4606-0

[…] amino acid alignments using this evolutionary model in raxml v8 on the ucr hpcc cluster with 1000 bootstraps [–]. a collapsed tree was also constructed from the three- and four- species trees in treegraph 2 by collapsing any node with < 70% bootstrap support into a polytomy []., protein domains were investigated using multiple online programs including, interpro […]

PMCID: 5874252
PMID: 29593259
DOI: 10.1038/s41426-018-0046-9

[…] the robustness of the ml trees using raxml version 8.0 (ref. ). ml inference was repeated at least three times per dataset to assure tree topology was maintained. final trees were constructed using treegraph2 and figtree v1.4.3 (ref. ). for the analysis of internal genes, we obtained all publicly available genes of wild bird origin obtained between 1976 and 2017 from eurasia and the americas. […]

PMCID: 5846723
PMID: 29529094
DOI: 10.1371/journal.pone.0192502

[…] tree, and tracecomp reporting a maximum discrepancy < 0.08 with effective sizes > 500. to create , the support values from the two bayesian analyses were mapped onto the ml tree using treegraph2 (version 2.13) []. branches were thickened if their bipartition received significant support in at least one analysis, and thickened greatly if they were significantly supported […]

PMCID: 5869500
PMID: 29498637
DOI: 10.3390/v10030107

[…] [], with 1000 bootstrap replicates used to infer branch support and rooted with two swan circovirus sequences (eu056309, eu056310). branches with less than 60% support were collapsed using treegraph2 []., the gocv, picv, and bfdv gene sequences were all initially codon aligned within a singled data set so as to ensure that homologous codon sites could be accurately compared to one […]

PMCID: 5812252
PMID: 29479366
DOI: 10.3389/fpls.2018.00142

[…] ; ). both ml and bi analyses, as well as jmodeltest, were performed at the cipres science gateway., phylogenetic incongruence between ml and bi analyses of each dataset was visually compared using treegraph version 2.12 (). the incongruence length difference test (ild) () was not used to assess topological conflict between the nuclear and the concatenated plastid datasets because this analysis […]


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

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