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JTreeView specifications

Information


Unique identifier OMICS_13097
Name JTreeView
Alternative name Java based Phylogenetic Tree Viewer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 0.8
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Tancred Frickey

JTreeView citations

 (207)
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STT3 dependent PD L1 accumulation on cancer stem cells promotes immune evasion

2018
Nat Commun
PMCID: 5954021
PMID: 29765039
DOI: 10.1038/s41467-018-04313-6
call_split See protocol

[…] 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 on the basis of the measured fluorescence ratio. For […]

library_books

Effect of Bmi1 over expression on gene expression in adult and embryonic murine neural stem cells

2018
Sci Rep
PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] 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 after personal commu […]

library_books

Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors

2018
BMC Genomics
PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] unn’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 (http://jtreeview.sourceforge.net).To study protein sequence divergence according to more specific GO terms, the whole set of GO 1:1 orthologs (isotig-dataset) was subdivided into equal terciles according to […]

library_books

Global analysis of genetic circuitry and adaptive mechanisms enabling resistance to the azole antifungal drugs

2018
PLoS Genet
PMCID: 5922528
PMID: 29702647
DOI: 10.1371/journal.pgen.1007319

[…] 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 (http://jtreeview.sourceforge.net). 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 in 96-well plates, and grown at 30 […]

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Transcriptomic profiling of tall fescue in response to heat stress and improved thermotolerance by melatonin and 24 epibrassinolide

2018
BMC Genomics
PMCID: 5870388
PMID: 29587632
DOI: 10.1186/s12864-018-4588-y
call_split See protocol

[…] program (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm) using an uncentered matrix and complete linkage method []. The resulting tree figures were displayed using Java Treeview (http://jtreeview.sourceforge.net/) as described by Chan et al. []. […]

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Small RNA sequencing identifies dynamic microRNA deregulation during skeletal muscle lineage progression

2018
Sci Rep
PMCID: 5844870
PMID: 29523801
DOI: 10.1038/s41598-018-21991-w
call_split See protocol

[…] edian centering of expression level for each miRNA, clustering was perform using centered Pearson correlation with 1,000 iterations. The corresponding heatmap was generated using JavaTreeView (http://jtreeview.sourceforge.net).For the mRNA/miRNA correlation analyses, data from Targetscan 7 database were filtered using in-house scripts using stringency in the number of sites and Total context++ sco […]

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JTreeView institution(s)
University of Konstanz, Konstanz, Germany

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