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Protocols

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

Versioning


No version available

Documentation


Publication for HyperTree

HyperTree citations

 (24)
library_books

Diurnal Cycling Transcription Factors of Pineapple Revealed by Genome Wide Annotation and Global Transcriptomic Analysis

2017
Genome Biol Evol
PMCID: 5737478
PMID: 28922793
DOI: 10.1093/gbe/evx161

[…] ntpellier.fr/phyml-sms/; 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 (). […]

library_books

Self (in)compatibility in apricot germplasm is controlled by two major loci, S and M

2017
BMC Plant Biol
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. […]

call_split

Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s

2016
Sci Rep
PMCID: 5018878
PMID: 27616185
DOI: 10.1038/srep33099
call_split See protocol

[…] ree/). In this study, the phylogenetic tree of 1 772 mycobacterial P450s was viewed by iTOL (http://itol.embl.de/upload.cgi), and the phylogenetic tree of 17 598 P450s from 113 families was viewed by Hypertree 1.2.2. […]

call_split

Chemoproteomic Profiling of Lysine Acetyltransferases Highlights an Expanded Landscape of Catalytic Acetylation

2014
J Am Chem Soc
PMCID: 4227742
PMID: 24836640
DOI: 10.1021/ja502372j
call_split See protocol

[…] S3 (). A pairwise alignment was generated using Clustal Omega, and a phylogenic tree was constructed using the neighbor-joining method. All phylogenetic trees were displayed in hyperbolic space using Hypertree, with branches of the tree designated by different colors and labeled by name where appropriate. […]

library_books

Identification and Functional Characterisation of CRK12:CYC9, a Novel Cyclin Dependent Kinase (CDK) Cyclin Complex in Trypanosoma brucei

2013
PLoS One
PMCID: 3689728
PMID: 23805309
DOI: 10.1371/journal.pone.0067327

[…] w.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) 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) . HyperTree software was used to format the output of the phylogenetic trees . […]

library_books

Injury elicited stressors alter endogenous retrovirus expression in lymphocytes depending on cell type and source lymphoid organ

2013
BMC Immunol
PMCID: 3562510
PMID: 23289855
DOI: 10.1186/1471-2172-14-2

[…] ro 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*, 4/4 […]

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

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