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tred specifications

Information


Unique identifier OMICS_10853
Name tred
Alternative name tree editor
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Javascript, Python
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


tred citations

 (31)
library_books

SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells

2018
Clin Epigenetics
PMCID: 5833080
PMID: 29507647
DOI: 10.1186/s13148-018-0460-9

[…] SERPINB9 CpG Island which is located in the gene body), promoters and transcriptional start sites were identified using the transcriptional regulatory element promoter database (http://rulai.cshl.edu/TRED) and the NCBI gene database (https://www.ncbi.nlm.nih.gov/gene). All candidate gene sequences (GRCh38) were compiled in a single file for use as an in-house reference sequence for bioinformatics […]

library_books

A Hybrid Model for Safety Pharmacology on an Automated Patch Clamp Platform: Using Dynamic Clamp to Join iPSC Derived Cardiomyocytes and Simulations of Ik1 Ion Channels in Real Time

2018
Front Physiol
PMCID: 5782795
PMID: 29403387
DOI: 10.3389/fphys.2017.01094

[…] ster or the Patchliner PatchControlHT software used to run experiments, and can be set automatically using the programming features in these software programs (i.e., Protocol Editor in PatchMaster or Tree Editor in PatchControlHT). […]

library_books

Probing Genomic Aspects of the Multi Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

2017
Front Microbiol
PMCID: 5733095
PMID: 29312194
DOI: 10.3389/fmicb.2017.02485

[…] s; Maximum-Likelihood (ML) tree was constructed using PhyML v3.0 (Guindon et al., ), GTR model and supported by Approximate Likelihood Ratio Test (aLRT). Interactive Tree of Life (iTOL) was used as a tree editor to assign clade and annotate metadata (Letunic and Bork, ). […]

call_split

Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi

2017
Redox Biol
PMCID: 5384416
PMID: 28391181
DOI: 10.1016/j.redox.2017.03.026
call_split See protocol

[…] n with rate heterogeneity modeled by a GAMMA distribution and 1000 rapid bootstrap resampled estimates of log-likelihood (RELL bootstrap). The resulting phylogeny was prepared for visualization using Tree Editor from the MEGA 7 software . […]

library_books

Automatic classification of histopathological diagnoses for building a large scale tissue catalogue

2016
PMCID: 5346425
PMID: 28344914
DOI: 10.1007/s12553-016-0169-8

[…] ation is not reachable.Currently we have a set of 104 classification trees with an overall number of 4285 nodes shown in Fig. . These classification trees were created with the help of an interactive tree editor and an ontology-based term extraction tool by medical experts at the Institute of Pathology in Graz. Figure shows the outline of the complete tree for the classification of ICD-10 codes a […]

library_books

Diversity, Mutation and Recombination Analysis of Cotton Leaf Curl Geminiviruses

2016
PLoS One
PMCID: 4872795
PMID: 26963635
DOI: 10.1371/journal.pone.0151161

[…] was constructed, using the Maximum likelihood method with 1000 bootstrap replications. The branches of identical molecules or isolates within a species were converted into a colored triangle by using Tree Editor of MEGA6 []. The phylogenetic tree was constructed with 191 sequences (BYVMV = 74, CLCuALV = 8, CLCuMuV = 58, CLCuKoV = 40, PaLCuV = 10, ACMV = 1). For determining the percent nucleotide i […]

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