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HyperTree specifications

Information


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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Documentation


Publication for HyperTree

HyperTree in pipelines

 (3)
2013
PMCID: 3562510
PMID: 23289855
DOI: 10.1186/1471-2172-14-2

[…] version 8.1.2 (dnastar, madison, wi). multiple sequence alignment of the 100 unique u3s was performed using the clustal w method in megalign (dnastar), and a phylogenetic tree was generated by the hypertree program []. seven u3 sequences, representing the seven phylogenetic branches, were subjected to a multiple alignment analysis to examine the u3 sequence features of direct repeats (1/1*, […]

2007
PMCID: 2323293
PMID: 17907803
DOI: 10.1371/journal.ppat.0030136

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

2006
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 (). each subfamily was individually examined for redundancy and further internal structure (data not shown)., each subfamily […]


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HyperTree in publications

 (14)
PMCID: 5737478
PMID: 28922793
DOI: 10.1093/gbe/evx161

[…] last accessed august 30, 2017) (). branch support values were calculated using the sh-like approximate likelihood ratio test (alrt). the resulting trees were visualized using hypertree v1.2.2 ()., compiled a comprehensive list of 67 tf families and 29 tc families based on the survey of signature domains in all available tf databases and other resources, and identified […]

PMCID: 5405505
PMID: 28441955
DOI: 10.1186/s12870-017-1027-1

[…] phyton script. bootstrapped data matrices were obtained using the phyltools 1.32 software [] and used to test the stability of the neighbor joining trees constructed with the phylip 3.62 package []. hypertree software [] was used to visualize the obtained trees., additional file 1: table s1. additional file 2: table s2. additional file 3: table s3. additional file 4: table s4. additional file […]

PMCID: 3562510
PMID: 23289855
DOI: 10.1186/1471-2172-14-2

[…] version 8.1.2 (dnastar, madison, wi). multiple sequence alignment of the 100 unique u3s was performed using the clustal w method in megalign (dnastar), and a phylogenetic tree was generated by the hypertree program []. seven u3 sequences, representing the seven phylogenetic branches, were subjected to a multiple alignment analysis to examine the u3 sequence features of direct repeats (1/1*, […]

PMCID: 3527207
PMID: 23284297
DOI: 10.1371/journal.pgen.1003129

[…] algorithm . the best-scoring ml trees were visualized and annotated in figtree version 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree). strain identifiers in major clades were selected using hypertree version 1.2.2 . bootstrap maximum likelihood trees in newick format can be found in dataset s2., we predicted the presence or absence of is5 transposons in wolbachia genomes at two loci […]

PMCID: 3416854
PMID: 22900041
DOI: 10.1371/journal.pone.0042702

[…] obtained from complementary values of pair-wise identity-by-state. a neighbour-joining tree was constructed using phylip (http://evolution.genetics.washington.edu/phylip.html) and visualized with hypertree , a java phylogenetic tree viewer (http://kinase.com/tools/hypertree.html)., we knew there was a familial structure in the xavante indians sample. genealogical relationships […]


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

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