TreeViewX protocols

View TreeViewX computational protocol

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TreeViewX specifications

Information


Unique identifier OMICS_13038
Name TreeViewX
Alternative name TreeView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format NEXUS,NEWICK
Output format NEXUS,NEWICK
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Version 0.5
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Roderic Page <>
  • person_outline Rod Page <>

Additional information


http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/

Publications for TreeViewX

TreeViewX in pipelines

 (11)
2017
PMCID: 5247444
PMID: 28163698
DOI: 10.3389/fmicb.2017.00022

[…] 200 bootstrap replicates. a tree was built from each replicate with the dnadist program, and then bootstrap values were computed with the consense program. the phylogenetic tree was visualized with treeviewx (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html). the programs used to construct the phylogenetic tree were obtained from the phylip package, v.3.65 (felsenstein, ), […]

2017
PMCID: 5544203
PMID: 28777807
DOI: 10.1371/journal.pone.0182484

[…] were subsequently predicted using the program prodigal version 2.6.1 []. sequences were aligned and phylogenetic trees were constructed with clustalx version 2.1 [] and further visualised with treeviewx version 0.5.0 []., the nucleotide sequences analysed in the current study are deposited in genbank (see for genbank accession numbers)., in order to study the expression rate […]

2015
PMCID: 4594746
PMID: 26437919
DOI: 10.1186/s12864-015-1953-y

[…] difference. a heatmap was produced by analyzing the expression abundance of lncrna genes with the software clustering []. the average linkage method was used and the results were viewed using java treeview []. if the expression of a lncrna meets following criteria, we defined it as the specifically-expressed lncrna: 1) the expression is > 3 fpkm in one sample whereas it is < 1 fpkm […]

2015
PMCID: 4619224
PMID: 26493074
DOI: 10.1186/s12864-015-2085-0

[…] to swap branches in the tree space with paup * 4b10 for 100 bootstraps [], with a hetequal character transition matrix, as previously described by james et al. []. trees were visualised by treeview []., validation of snps and indels was performed using an aliquot of the dna solution that was used to generate the illumina sequencing reads. primers were designed from flanking regions […]

2014
PMCID: 4227137
PMID: 25005139
DOI: 10.1186/bcr3689

[…] []. genes that were significantly differentially expressed by parity were clustered across all samples using average linkage hierarchical cluster analysis, and results were visualized using java treeview software []. ontology classification and pathway analyses were performed on the identified genes using gominer software []., the pbcs is a population-based case–control study conducted […]


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TreeViewX in publications

 (2681)
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w

[…] (similarity metric: correlation (uncentered), clustering method: average linkage) using the version 3.0 of cluster (open source clustering software), and visualized with the java-based program treeview, in order to assess similarities and differences among their expression patterns. here and in other heat maps utilized, genes with a null normalized expression value are log-transformed and, […]

PMCID: 5954140
PMID: 29765046
DOI: 10.1038/s41467-018-04244-2

[…] (national cancer institute, bethesda, md). gene expression differences were considered statistically significant if the p‐value was less than 0.001. cluster analysis was performed with cluster and treeview. kaplan–meier plots and log‐rank test were used to estimate patient prognoses., the genomic data are available from the ncbi gene expression omnibus (geo) under accession numbers (gse13861, […]

PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6

[…] in the “epithelial” arm (supplementary data ). a higher emt score indicates a more mesenchymal-like signature. to view the clustering results generated by cluster 3.0, we use alok saldanha’s java treeview [http://sourceforge.net/projects/jtreeview/], which can display both hierarchical and k-means clustering results. the heat map was represented graphically by coloring each samples […]

PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] at the galaxy server,. further analysis was performed using excel. clustering was performed using cluster 3.0 (http://bonsai.ims.utokyo.ac.jp/bmdehoon/software/cluster/) and visualized using java treeview (http://jtreeview.sourceforge.net/). gene ontology analysis was performed using the generic gene ontology term finder. for comparison with other data sets, data was downloaded or obtained […]

PMCID: 5934392
PMID: 29725014
DOI: 10.1038/s41467-018-04179-8

[…] total, 255 samples were included in the analysis., brb-array tools (national institutes of health) was primarily used for all statistical analyses. cluster analysis was performed using cluster and treeview v3.0 (ref. ). we identified genes whose expression was unique to the s cluster (mp subtype) by cross-comparing gene lists from independent statistical tests. we first generated two different […]


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TreeViewX institution(s)
Division of Environmental and Evolutionary Biology, University of Glasgow, UK

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