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Protocols

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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Versioning


No version available

Documentation


Maintainers


  • person_outline Roderic Page
  • person_outline Rod Page

Additional information


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

Publications for TreeViewX

TreeViewX citations

 (1288)
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Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds

2018
PLoS One
PMCID: 5919407
PMID: 29698497
DOI: 10.1371/journal.pone.0196276
call_split See protocol

[…] genetic distance [] among the populations was calculated and a neighbour-joining tree was reconstructed using the PHYLIP package version 3.6 []; the dendrogram was depicted using the software package TreeView version 1.6.6 []. Bootstrap values were obtained with 1,000 replicates over the loci.The hierarchical analysis of molecular variance (AMOVA) was performed using ARLEQUIN software version 3.5 […]

call_split

Urinary biomarkers predict advanced acute kidney injury after cardiovascular surgery

2018
PMCID: 5921971
PMID: 29699579
DOI: 10.1186/s13054-018-2035-8
call_split See protocol

[…] 12–30% and > 30% for the risk categories. A p value <0.05 was considered significant.Hierarchical clustering analysis was performed using the cluster program and the results were visualized using the Treeview program []. The biomarkers were arranged in such a way that the most similar expression profiles were placed next to each other. In the color scheme, strong positive staining is indicated as […]

library_books

An Evolutionarily Conserved Mechanism for Intrinsic and Transferable Polymyxin Resistance

2018
MBio
PMCID: 5893884
PMID: 29636432
DOI: 10.1128/mBio.02317-17

[…] A collection of MCR-like proteins were aligned using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/) (). The phylogenetic tree was generated and visualized using TreeView (). In addition to EptA, the MCR-like proteins included the following: MCR-1 and its 8 variants (); MCR-2 () plus its 2 variants, MCR-2.1 (accession number ASK49941) and MCR-2.2 (accession nu […]

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Alterations in the p53 SOCS2 axis contribute to tumor growth in colon cancer

2018
PMCID: 5940812
PMID: 29622769
DOI: 10.1038/s12276-017-0001-1
call_split See protocol

[…] in at least 10% of samples were selected for cluster analysis. Average linkage hierarchical cluster analysis was carried out using Pearson correlation as the similarity metric, using the GeneCluster/TreeView program (http://rana.lbl.gov/EisenSoftware.htm). We used t test P = 0.01. To ascertain biological relevance, a fold-change cutoff value of 1.5 from the mean was chosen. […]

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Transcriptional Regulation of the Peripheral Pathway for the Anaerobic Catabolism of Toluene and m Xylene in Azoarcus sp. CIB

2018
Front Microbiol
PMCID: 5874301
PMID: 29623071
DOI: 10.3389/fmicb.2018.00506
call_split See protocol

[…] ied out according to the Kimura two-parameter method (), and a tree was reconstructed using the neighbor-joining method () of the PHYLIP program () at the TreeTop-GeneBee server and represented using TreeView X 0.5.1 (Glasgow University). […]

library_books

Human Antibody Responses to Emerging Mayaro Virus and Cocirculating Alphavirus Infections Examined by Using Structural Proteins from Nine New and Old World Lineages

2018
PMCID: 5863033
PMID: 29577083
DOI: 10.1128/mSphere.00003-18

[…] s BioNJ with optimization by using tree topology and branch length and tree improvement using subtree pruning and regrafting. Phylogram images were generated by using the Newick format tree output in TreeView v1.6.6 (). […]

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

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