Tag: Calculation

DASS – Discovery and P-value Calculation of Substructures in Unordered data

DASS

:: DESCRIPTION

DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASSSub) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASSPset), or for sets with multiple occurrence of elements (DASSPmset).

::DEVELOPER

Dr. Maik Friedel , J.Hollunder

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  DASS

:: MORE INFORMATION

Citation

DASS: Efficient Discovery and P-Value Calculation of Substructures in Unordered Data
Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm
Bioinformatics (2007), 23(1): 77-83.

 

FDDH – pKa calculations with the FD/DH method

FDDH

:: DESCRIPTION

FDDH is a software of pKa calculations with the FD/DH method

::DEVELOPER

Warwicker Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Fortron

:: DOWNLOAD

  FDDH 

:: MORE INFORMATION

Citation

Proteins. 2011 Dec;79(12):3374-80. doi: 10.1002/prot.23078. Epub 2011 Jun 9.
pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.
Warwicker J.

PedPeel 0.0.2 – Prepare Pedigree data for Calculation of Elston-Stewarts’ Likelihood function

PedPeel 0.0.2

:: DESCRIPTION

PedPeel prepares pedigree data for calculation of Elston-Stewarts’ likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 PedPeel

:: MORE INFORMATION

Citation:

Comput Biol Chem. 2007 Jun;31(3):173-7. Epub 2007 Mar 24.
Optimal peeling order for pedigrees with incomplete genotypic information.
Belonogova NM, Axenovich TI.

JOINMAP 4.1 – Calculation of Genetic Linkage Maps

JOINMAP 4.1

:: DESCRIPTION

JOINMAP is a software for the calculation of genetic linkage maps in experimental populations of diploid species. JoinMap provides high quality tools that allow detailed study of the experimental data and the generation of publication-ready map charts. The intuitive MS-Windows ? user interface of JoinMap invites to a better exploration of the data. For instance, you can perform several diagnostical tests, both before and after the actual map calculation, and you can remove potentially erroneous loci and individuals from the map calculations by a simple mouse-click.

::DEVELOPER

Kyazma B.V.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 JOINMAP

:: MORE INFORMATION

Citation

Stam, 1995.
JoinMap 2.0 deals with all types of plant mapping populations.
Plant Genome III Abstracts

permuteP 1.4 – Permutation P-value Calculation

permuteP 1.4

:: DESCRIPTION

permuteP exacts permutation p-value calculation for case-control study of collapsoing a group of rare SNPs, and approximate permutation p-value calculation for QTL mapping in experimental cross

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

   permuteP

:: MORE INFORMATION

KinInbcoef 1.1 – Calculation of Kinship and Inbreeding Coefficients

KinInbcoef 1.1

:: DESCRIPTION

KinInbcoef is a C++ program that computes inbreeding and kinship coefficients for general pedigrees

::DEVELOPER

Catherine Bourgain, Qian Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

 KinInbcoef

:: MORE INFORMATION

KinInbcoefX 2.0 – Calculation of X-chromosome Kinship Coefficients

KinInbcoefX 2.0

:: DESCRIPTION

KinInbcoefX is a C++ program that calculates X-chromosome kinship coefficients for pairs of individuals (and X-chromosome inbreeding coefficients for each individual), based on pedigree and sex information.

::DEVELOPER

Qian Zhang, Catherine Bourgain,  Mary Sara McPeek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

  KinInbcoefX

:: MORE INFORMATION

PATERN – Calculation of Paternity Probabilities

PATERN

:: DESCRIPTION

PATERN is a computer program for the calculation of paternity probabilities from the multilocus DNA profiles of trios, comprising mother, child and putative father.

::DEVELOPER

 Michael Krawczak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PATERN

:: MORE INFORMATION

Citation:

Krawczak M, Bockel B (1992)
A genetic factor model for the statistical analysis of multilocus DNA fingerprints.
Electrophoresis 13: 10-17.

EASYPAT 8.3 – Calculation of Likelihood Ratios for Single Locus data

EASYPAT 8.3

:: DESCRIPTION

EASYPAT is a computer program that allows calculation of likelihood ratios for single locus data, comparing specific types of simple hypotheses regarding the familial relationships involved.

::DEVELOPER

 Michael Krawczak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 EASYPAT

:: MORE INFORMATION

AtVol 1.2 – Atomic Volume Calculation

AtVol 1.2

:: DESCRIPTION

AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

AtVol

:: MORE INFORMATION

AtVol is free software available under the terms of its own BSD-style license.