ABC4F 1.0 – Approximate Bayesian Computation for F-statistics

ABC4F 1.0

:: DESCRIPTION

ABC4F (Approximate Bayesian Computation for F-statistics) is a free software that estimates F-statistics using dominant data. The method implemented in ABC4F corrects for the ascertainment biases that characterise AFLP markers.

::DEVELOPER

Laboratoire d’Ecologie Alpine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ABC4F

:: MORE INFORMATION

Citation

Foll, M, M.A. Baumont and O.E. Gaggiotti, 2008.
An Approximate Bayesian Computation approach to overcome biases that arise when using AFLP markers to study population structure.
Genetics, 179:927-939.

GenMap 1.3.0 – Fast and Exact Computation of Genome Mappability

GenMap 1.3.0

:: DESCRIPTION

GenMap computes the uniqueness of k-mers for each position in the genome while allowing for up to e mismatches.

::DEVELOPER

Christopher Pockrandt

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

GenMap

:: MORE INFORMATION

Citation

Pockrandt C, Alzamel M, Iliopoulos CS, Reinert K.
GenMap: ultra-fast computation of genome mappability.
Bioinformatics. 2020 Jun 1;36(12):3687-3692. doi: 10.1093/bioinformatics/btaa222. PMID: 32246826; PMCID: PMC7320602.

DTWave 201405 – Dynamic Time Warping for Spectrogram Alignment and AVErage Sequence Computation

DTWave 201405

:: DESCRIPTION

DTWave is a tool for analysing sound sequences, it allows to
– measure a pairwise distance between two or more sounds,
– compute an average sequence from a pair of sounds.

::DEVELOPER

the New Zealand Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C Compiler

:: DOWNLOAD

 DTWave

:: MORE INFORMATION

Citation:

Louis Ranjard, Michael G. Anderson, Matt J. Rayner, Robert B. Payne, Ian McLean, James V. Briskie, Howard A. Ross, Dianne H. Brunton, Sarah M. N. Woolley, Mark E. Hauber,
Bioacoustic distances between the begging calls of brood parasites and their host species: a comparison of metrics and techniques,
Behavioral Ecology and Sociobiology, 2010

WEBnm@ 3.3 – Web-server for Normal Mode Analysis of proteins

WEBnm@ 3.3

:: DESCRIPTION

WEBnm@ is meant to provide users with simple and automated computation and analysis of low-frequency normal modes for proteins.

::DEVELOPER

Reuter Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Dec 30;15(1):6597. [Epub ahead of print]
WEBnm@ v2.0: Web server and services for comparing protein flexibility.
Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N.

WEBnm@: a web application for normal mode analysis of proteins.
S.M.Hollup, G.Salensminde and N.Reuter.
BMC Bioinformatics (2005), 6(1): 52

iTagPlot 1.0 – Computation and Interactive Visualization of Tag Density

iTagPlot 1.0

:: DESCRIPTION

iTagPlot is a tool to accurately compute and interactively visualize tag density (read coverage)from genomic sequencing data.

::DEVELOPER

iTagPlot team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • JRE

:: DOWNLOAD

 iTagPlot

:: MORE INFORMATION

Citation

iTagPlot: An accurate computation and interactive drawing tool for tag density plot.
Kim SH, Ezenwoye O, Cho HG, Robertson KD, Choi JH.
Bioinformatics. 2015 Mar 19. pii: btv166

POWER 3.0 – Computation of Sample Size and Power for Binary Outcome Studies

POWER 3.0

:: DESCRIPTION

POWER is a windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene X exposure interactions).

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  POWER

:: MORE INFORMATION

Citation

Garcia-Closas, Lubin (1999),
Power and sample size calculations in case-control studies of gene-environmental interactions: Comments on different approaches“,
American Journal of Epidemiology, 149:689-693.

zipHMM 1.0.1 – Library for very fast Likelihood Computations for Hidden Markov Models

zipHMM 1.0.1

:: DESCRIPTION

zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 zipHMM

:: MORE INFORMATION

Citation:

zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A, Kristiansen M, Pedersen CN, Mailund T.
BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.

QDist 2.0.2 – Computation of Quartet Distance between Evolutationary Trees

QDist 2.0.2

:: DESCRIPTION

QDist implements a sub-cubic algorithm for computing the quartet distance between general trees (i.e. the trees are not required to be binary).

::DEVELOPER

QDist team

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 QDist

:: MORE INFORMATION

Citation:

T. Mailund and C.N.S. Pedersen,
QDist—Quartet Distance Between Evolutionary Trees,
Bioinformatics, Vol. 20, No. 10, pp 1636-1637, 2004.

FluxModeCalculator – Large-scale Flux mode Computation

FluxModeCalculator

:: DESCRIPTION

FluxModeCalculator is a MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models

::DEVELOPER

Jan Bert van Klinken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 FluxModeCalculator

:: MORE INFORMATION

Citation

FluxModeCalculator: an efficient tool for large-scale flux mode computation.
van Klinken JB, Willems van Dijk K.
Bioinformatics. 2015 Dec 18. pii: btv742.

TFM-Pvalue 0.0.8 – Efficient and Accurate P-value Computation for Position Weight Matrices

TFM-Pvalue 0.0.8

:: DESCRIPTION

TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R

 TFM-Pvalue

:: MORE INFORMATION

Citation

Efficient and accurate P-value computation for Position Weight Matrices
H. Touzet and J.S. Varré
Algorithms for Molecular Biology 2007, 2:15

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