TreeView protocols

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TreeView specifications


Unique identifier OMICS_01574
Name TreeView
Alternative names Java Treeview, JavaTreeView
Software type Package/Module
Interface Command line 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 1.1.6
Stability Stable
Maintained Yes



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  • person_outline Alok Saldanha <>

Publications for TreeView


Java Treeview—extensible visualization of microarray data.

2004 Bioinformatics
DOI: 10.1093/bioinformatics/bth349

TreeView in pipelines

PMCID: 5840673
PMID: 29552123
DOI: 10.3892/ol.2018.7971

[…] 2nd, 2017). the pearson's correlation coefficient was performed using cluster 3.0 with average linkage in order to achieve the hierarchical heatmap (). analysis results were visualized employing the java treeview 1.1.6 version ()., the search tool for the retrieval of interacting genes (string; version 10.0) covers 5,214,234 proteins from 1,133 organisms (). in the present study, to evaluate […]

PMCID: 5913804
PMID: 29685105
DOI: 10.1186/s12870-018-1276-7

[…]  < 0.05 and < 0.01. cluster analysis of transcriptional profiles was performed using cluster software ( the heatmap was generated by java treeview 4 software []., promoter sequences were predicted using bioedit software ( and confirmed using blastp at ncbi (https://blast.ncbi.nlm.nih.go […]

PMCID: 5245798
PMID: 28103240
DOI: 10.1371/journal.pgen.1006538

[…] to the x. laevis genome v9.1 with bwa mem. topological domain peakfiles, interaction matrices, and metagene plots were generated with homer (additional details below). matrices were visualized with java treeview., all tads and significant interactions were called against a background of expected interactions. this background model was constructed using the approach described in []. briefly, […]

PMCID: 5301350
PMID: 28183269
DOI: 10.1186/s12864-016-3479-3

[…] clustering analysis was performed for differentially expressed unigenes from both tall fescue cultivars. the rpkm counts for each unigene were clustered using the software cluster 3.0, and java treeview was applied to view the cluster image. finally, java treeview was used to visualize the results []., to validate the expression of the target genes, qrt-pcr was carried out using […]

PMCID: 5312943
PMID: 28207760
DOI: 10.1371/journal.pone.0170870

[…] modules were ordered by temporal expression and mrna similarity within modules was determined with cluster 3.0 using average-linkage centered pearson correlation and results were visualized with java treeview []., coding sequences for 810 micronuclear-derived mrnas plus annotated macronuclear rnas were combined and expression levels (tpm) were determined with kallisto under default settings […]

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TreeView in publications

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

[…] genes 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 [], 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 ( and visualized using java treeview ( gene ontology analysis was performed using the generic gene ontology term finder. for comparison with other data sets, data was downloaded […]

PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] one-way anova test with dunn’s correction for multiple comparisons. z values were hierarchically clustered using cluster 3.0 [] according to species and graphically represented as heatmaps using java treeview 1.1.6r4 (, to study protein sequence divergence according to more specific go terms, the whole set of go 1:1 orthologs (isotig-dataset) was subdivided […]

PMCID: 5921755
PMID: 29699519
DOI: 10.1186/s12885-018-4409-3

[…] for each gene) were used to adjust for abundance differences across samples, and differentially expressed genes (degs) were extracted. the normalized gene counts were imported into cluster3.0 and java treeview (version 1.1.6r4) for hierarchical clustering analysis and visualization. enriched pathway and functional classification analyses of differences in expression of degs were performed […]

PMCID: 5922528
PMID: 29702647
DOI: 10.1371/journal.pgen.1007319

[…] optical density values of technical duplicate measurements. each strain was tested in duplicate in three biological replicates. mic data was quantitatively displayed with color using the program java treeview 1.1.3 ( for growth kinetics assays, cultures were grown overnight in ypd, diluted to an od600 of 0.1 in 100 μl of ypd without or with fluconazole […]

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TreeView institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
TreeView funding source(s)
Supported by a National Defense Science and Engineering Graduate Fellowship, the Stanford Genome Training Program (Training Grant NIH 5 T32 HG00044) and NIH grants HG 01315 and GM 46406.

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