TreeViewX protocols

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description
TreeViewX computational protocol

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
Source code URL http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/download/0.5/tv-0.5.1.tar.gz
Maintained Yes

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Documentation


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

 (4)
2017
PMCID: 5422468
PMID: 28536556
DOI: 10.3389/fmicb.2017.00772

[…] 1 min, 55°c for 1 min, and 72°c for 10 min. the 16s rrna gene fragment (1450 bp length) was sequenced. multiple sequence alignment and molecular phylogeny were performed using bioedit 7.0.5.3 and treeviewx., glutathione content was determined as previously described in the cell lysate of l. plantarum isolate (l7) following growth in mrs broth at 37°c under anaerobic conditions. growth curve […]

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

[…] were subsequently predicted using the program prodigal version 2.6.1 [90]. sequences were aligned and phylogenetic trees were constructed with clustalx version 2.1 [91] and further visualised with treeviewx version 0.5.0 [92]., the nucleotide sequences analysed in the current study are deposited in genbank (see s7 table for genbank accession numbers)., in order to study the expression rate […]

2010
PMCID: 2887360
PMID: 20567509
DOI: 10.1371/journal.pone.0011164

[…] 2cp-c (adeh). multiple sequence alignments and bootstrap trees with 1000 replicates were generated using clustalx2 [59] and the neighbour-joining method [60]. trees were visualized using the program treeview x. [61]. domain informations are given as pfam numbers and domain organizations were analyzed using the conserved domains database (cdd, http://www.ncbi.nlm.nih.gov/structure/cdd/). […]

2010
PMCID: 2996925
PMID: 20565988
DOI: 10.1186/1471-2164-11-392

[…] gene, relevant amino acid sequences were aligned, a phylogenetic tree was constructed using quartet puzzling algorithm implemented in the tree-puzzle program [39], and the result was visualized by treeviewx [40]. our analysis suggests that the zebrafish has genes coding for rennin, nothepsin and several members of cathepsins (figure 5). however, none of these zebrafish genes resemble […]

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

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