HyperTree protocols

HyperTree computational protocol

HyperTree specifications


Unique identifier OMICS_04814
Name HyperTree
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


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Publication for HyperTree

HyperTree IN pipelines

PMCID: 3689728
PMID: 23805309
DOI: 10.1371/journal.pone.0067327

[…] or via the website www.kinase.com. cyclin and kinase domains were then aligned and bootstrap neighbour joining trees were generated using clustalx (1.81) [31]. hypertree software was used to format the output of the phylogenetic trees [32]., t. brucei brucei strain lister 427 wildtype cell lines (procyclic and bloodstream stages), lister 427 phd449 [33] […]

PMCID: 1821060
PMID: 17355176
DOI: 10.1371/journal.pbio.0050077

[…] was then computed with muscle [94]. distance based phylogenies were computed using the programs dnadist and neighbor from the phylip package [95] using default settings. trees were visualized using hypertree [96]., based on the low-identity overlap database described above, the similarity of a library i to another library j at a given percent identity cutoff was computed as follows. […]

PMCID: 1857360
PMID: 17242065
DOI: 10.1083/jcb.200604106

[…] (version 7; accelrys) followed by phylogenetic analysis using protdist and neighbor present in the phylip 3.6 package (http://evolution.genetics.washington.edu/phylip.html). the tree was drawn using hypertree (bingham and sudarsanam, 2000)., fig. s1 shows that deletion of the vacuolar peptidase pep4 or incubation of yeast cells with pmsf results in the accumulation of kinases rim11 and tpk2 […]

PMCID: 2323293
PMID: 17907803
DOI: 10.1371/journal.ppat.0030136

[…] phylogenetic analysis based upon the number of differences using the mega3 program [68]. furthermore, only parsimonious informative sites were considered. the phylogenetic tree was displayed using hypertree java program [69]., tbsider1 (ten), tbsider2 (12), rime (70), and nartc (115) sequences were separately aligned using clustalw (http://www.ebi.ac.uk/tools/clustalw/), whereas lmsider2 […]

PMCID: 1474054
PMID: 16738128
DOI: 10.1093/nar/gkl295

[…] not be reasonably aligned. an overview of a neighbour-joining tree constructed from a multiple alignment excluding the variable minor and major insertion regions (see text) and visualized using hypertree demonstrates the clearly distinguishable division of subfamilies (figure 1b). each subfamily was individually examined for redundancy and further internal structure (data not shown)., […]

HyperTree institution(s)
SUGEN, South San Francisco, CA, USA

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