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Number of citations per year for the bioinformatics software tool T-BAS
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Protocols

T-BAS specifications

Information


Unique identifier OMICS_14381
Name T-BAS
Alternative name Tree-Based Alignment Selector
Interface Web user interface
Restrictions to use None
Input data Curated alignments of sequence data for the selected taxa or a FASTA formatted file with unknown query sequences.
Input format FASTA
Output data Separate or concatenated alignments.
Output format PHYLIP, FASTA, XML, CSV, NEXUS
Programming languages Javascript, PHP, Python
Computer skills Basic
Version 1.0
Stability Stable
Maintained No

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Publication for Tree-Based Alignment Selector

T-BAS citations

 (8)
call_split

Global population structure and adaptive evolution of aflatoxin‐producing fungi

2017
Ecol Evol
PMCID: 5677503
PMID: 29152206
DOI: 10.1002/ece3.3464
call_split See protocol

[…] on A. flavus and A. parasiticus isolates and their associated chemotype profiles. Phylogenies were displayed in circle tree format using FigTree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/) or T‐BAS v2.0 (Carbone, unpublished), an extension of the T‐BAS v1.0 toolkit (Carbone et al., ). Clade groupings were labeled along the tree perimeter based on species or morphotype (e.g., A. flavus L, A […]

library_books

Dynamics of hybrid switching DS I A epidemic model

2017
Sci Rep
PMCID: 5615109
PMID: 28951546
DOI: 10.1038/s41598-017-11901-x

[…] sexual partner, α > 0 is the is the susceptibility of susceptible individuals and βα > 0 becomes the average number of effective contacts of one infective individual per unit time:1.1{dS(t)dt=μ(S0−S(t))−βαS(t)I(t)N(t),dI(t)dt=βαS(t)I(t)N(t)−(μ+γ)I(t),dA(t)dt=γI(t)−δA(t),where the parameters μ, S 0, α, γ and δ∈ℝ+. () assume a homogeneous susceptible population such that there is one group of susce […]

library_books

Repression of intestinal transporters and FXR FGF15 signaling explains bile acids dysregulation in experimental colitis associated colon cancer

2017
Oncotarget
PMCID: 5609951
PMID: 28969019
DOI: 10.18632/oncotarget.18885

[…] Because UGTs mediated BAs glucuronidation in the ileum remained largely unchanged, we sought to determine the transporters involved in the uptake of BAs. We found taurine-conjugated BAs (T-BAs), which are dominant in the ileum, were markedly decreased in ileum while generally accumulated in other compartments of AOM/DSS-treated mice (Figure ). The uptake of T-BAs in the ileum depends […]

call_split

Wood staining fungi revealed taxonomic novelties in Pezizomycotina: New order Superstratomycetales and new species Cyanodermella oleoligni

2016
PMCID: 5198870
PMID: 28050056
DOI: 10.1016/j.simyco.2016.11.008
call_split See protocol

[…] the “dark” group were added to the six-locus supermatrix (5.8S, nrLSU, nrSSU, mitSSU, RPB1, RPB2) used to generate the most comprehensive phylogeny for Pezizomycotina (986 taxa) as part of the online T-BAS tool (http://tbas.hpc.ncsu.edu; Carbone et al. unpubl. data). We also completed analyses on the same data set but our fungal strains were represented by the ribosomal (Analysis 2A; 5.8S, nrLSU, […]

library_books

A new method for the extraction of fetal ECG from the dependent abdominal signals using blind source separation and adaptive noise cancellation techniques

2015
PMCID: 4650367
PMID: 26576777
DOI: 10.1186/s12976-015-0021-2

[…] it is not enough to estimate the mixing matrix, through (). The estimated source signals obtained by a direct BSS, for the noisy case, can be written as follows (4)y¯(t):=nx¯(t):=y(t)+n¯(t),where y(t):=BAs(t) and n¯(t)=Bn(t). That is the noisy estimated source y¯(t) is the sum of y(t) the ideal estimated source, and the noise n¯(t). Ideally, we would like to retrieve y(t) by denoising y¯(t), but […]

library_books

Approximate Joint Diagonalization and Geometric Mean of Symmetric Positive Definite Matrices

2015
PLoS One
PMCID: 4412494
PMID: 25919667
DOI: 10.1371/journal.pone.0121423

[…] for s(t), without assuming any knowledge on the mixing matrix A (that is why it is named “blind”). The goal of BSS is to estimate the demixing matrix B yielding source estimates y(t) such as y(t)=Bx(t)=BAs(t), where we have ignored the noise term in () and where A is the unknown true mixing matrix. An important family of BSS problems are solved by estimating a number of matrices holding second-or […]


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T-BAS institution(s)
Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA; Department of Biology, Duke University, Durham, NC, USA; School of Plant Sciences, The University of Arizona, Tucson, AZ, USA; Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA; San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of Giessen, Giessen, Germany; Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA
T-BAS funding source(s)
Funding for the development of T-BAS was provided by the National Science Foundation (NSF) Dimensions of Biodiversity (DoB) (DEB-1046167, DEB-1045766 and DEB-1046065).

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