Tag: Calculate

silcLOD – Calculate Nominal Significance Levels and Critical LOD Scores

silcLOD

:: DESCRIPTION

silcLOD (significance levels and critical LODs) is designed to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified.

::DEVELOPER

Institute of Medical Biometry and Statistics, University of Lübeck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 silcLOD

:: MORE INFORMATION

Citation

E Lander, L Kruglyak (1995),
“Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results”,
Nature Genetics, 11:241-247.

PROBMAX 3n – Calculate Maximum Probability of Progeny Assignments

PROBMAX 3n

:: DESCRIPTION

PROBMAX calculates the maximum probability of progeny assignments to a mixture of possible contributing parents, when the genotypes of the parents are known and correspond to the genotypes screened in the progeny, and the parental mating combinations are known (or potentially known).

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PROBMAX

:: MORE INFORMATION

Citation

Danzmann, R.G. 1997.
PROBMAX: A computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny.
J. Hered. 88: 333.

RTP – Calculate Significance of Truncated Products of P-values

RTP

:: DESCRIPTION

RTP: C code for calculating significance of truncated products of P-values

::DEVELOPER

Frank Dudbridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C Compiler

:: DOWNLOAD

  RTP

:: MORE INFORMATION

Citation

Genet Epidemiol. 2003 Dec;25(4):360-6.
Rank truncated product of P-values, with application to genomewide association scans.
Dudbridge F, Koeleman BP.

GelyMac – Calculate DNA Fragment sizes from Gel Electrophoresis Migration data

GelyMac

:: DESCRIPTION

GelyMac is a program developed at Reed College which calculates DNA fragment sizes from gel electrophoresis migration data. GelyMac runs on a Macintosh computer only. The first step in using the GelyMac program is to enter data for a known marker. Both the distances traveled and the fragment sizes are entered. Then the distances migrated by up to 19 sets of DNA fragments are entered, and the program calculates the sizes of these fragments using a cubic-spline interpolation. These results are displayed on the screen and may also be printed.

::DEVELOPER

Biology Department, Reed College

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 GelyMac

:: MORE INFORMATION

Citation

Peter J. Russell, Joshua M. Doenias and Steven J. Russell
GELYMAC: a Macintosh application for calculating DNA fragment size from gel electrophoresis migration data
Comput Appl Biosci (1991) 7 (2): 265-266.

SURFace – Calculate Solvent accessible surface area

SURFace

:: DESCRIPTION

SURFace is a programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area. The accessible surface output is calculated for the whole molecule, per residue, and per atom.

::DEVELOPER

Barry Honig’s group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SURFace

:: MORE INFORMATION

Citation

  • Nicholls, A., Sharp, K. and Honig, B. Proteins (1991), 11:281
  • Sridharan, S., Nicholls, A., Honig, B. Biophys. J. (1992), 61:A174

DNAMIX 3.2 – Calculate Likelihood Ratios for Mixed DNA Samples Encountered in Forensic Science

DNAMIX 3.2

:: DESCRIPTION

DNAMIX is a computer program that will calculate likelihood ratios as they pertain to mixed DNA samples encountered in forensic science. Calculations are based on: Curran JM, Triggs CM, Buckleton J. Weir B.S. Interpreting DNA mixtures in structured populations.

::DEVELOPER

Gary W. Beecham Jr.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 DNAMIX

:: MORE INFORMATION

Citation

J Forensic Sci. 1999 Sep;44(5):987-95.
Interpreting DNA mixtures in structured populations.
Curran JM, Triggs CM, Buckleton J, Weir BS.

Annot 1.0 / PLINK2wakefieldBF 1.0 – Calculate Bayes Factors

Annot 1.0 / PLINK2wakefieldBF 1.0

:: DESCRIPTION

Annot / PLINK2wakefieldBF is a software for calculating Bayes Factors for combining functional annotation with association information, especially in the context of Genome-wide Association Studies.

PLINK2wakefieldBF.R = R function (Unix text format) for generating BFassoc values from PLINK output files

Annot.zip = Text file (Unix format) with BFannot values for each SNP in the combined Affy500+Illu550 panel + README file.

::DEVELOPER

 Dr Michael Weale’s Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 Annot / PLINK2wakefieldBF

:: MORE INFORMATION

Citation

Knight J, Barnes MR, Breen G, Weale ME,
“Using Functional Annotation for the Empirical Determination of Bayes Factors for Genome-wide Association Study Analysis”,
PLoS ONE 6(4): e14808. doi:10.1371/journal.pone.0014808

GeneticDistances 20090824 – Calculate common Genetic Distances for Allele Frequency data

GeneticDistances 20090824

:: DESCRIPTION

GeneticDistances is a program for my graduate students that calculates theta, Ds, and Da for genetic data in GENEPOP format

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 GeneticDistances

:: MORE INFORMATION

EI_EXCHANGE 1.0 – Calculate Elementary Mode

EI_EXCHANGE 1.0

:: DESCRIPTION

EI_EXCHANGE ( External and Internal Exchange) is a program to calculate elementary modes for the complete variety of external and internal metabolites and a program to calculate the approximated minimal number of mode.

::DEVELOPER

Department of Bioinformatics, Biocenter, University of Würzburg, Germany

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 EI_EXCHANGE for win, Source Code

:: MORE INFORMATION

Citation:

T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram, S. Schuster:
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.
BioSystems, 2003, 70, 255-270

CalSpec 1.3 – Calculate Spectra

CalSpec 1.3

:: DESCRIPTION

CalSpec (Calculate Spectra) is a software module for fast processing of mass spectrometric data in 13C Metabolic Flux Analysis(MFA). Efficient MFA requires a straightforward approach that can be parallelized and automated for all steps involved. A time-consuming and error prone step in the whole procedure of MFA is the extraction of labeling patterns from mass spectrometric spectra. CalSpec for identification of amino acids TBDMS derivates, addresses this problem and provides a software module for automated identification of specified analytes in the MS spectrum, quantification of labeling patterns and estimation of the analyte peak quality.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 CalSpec

:: MORE INFORMATION

Citation

Talwar P, Wittmann C, Lengauer T, & Heinzle E (2003)
Software tool for automated processing of 13C labeling data from mass spectrometric spectra.
Biotechniques 35(6):1214-1215.

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