TFPGA 1.3 – Analysis of Allozyme and Molecular Population Genetic data

TFPGA 1.3

:: DESCRIPTION

TFPGA (Tools for Population Genetic Analyses) is  a Windows program for the analysis of allozyme and molecular population genetic data. This program calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. Additional features include the ability to analyze hierarchical data sets as well as data from either codominant markers such as allozymes or dominant markers such as AFLPs or RAPDs.

::DEVELOPER

Mark P. Miller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TFPGA

:: MORE INFORMATION

Mykiss 20100426 – Estimates Reproductive Success and Parentage using Genetic Data.

Mykiss 20100426

:: DESCRIPTION

Mykiss is a computer program for estimating the reproductive success of individuals based on genetic data (codominant genotypes).

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 Mykiss

:: MORE INFORMATION

ML-Relate 20080422 – Estimating Relatedness or Relationship from Genetic data

ML-Relate 20080422

:: DESCRIPTION

ML-Relate is a computer program that calculates maximum likelihood estimates of relatedness and relationship. ML-Relate is designed for microsatellite data, and can accommodate null alleles. It uses simulation to perform two types of hypothesis tests.

::DEVELOPER

Steven Kalinowski, Ph.D.

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

  ML-Relate

:: MORE INFORMATION

Citation

Kalinowski ST, AP Wagner, ML Taper (2006).
ML-Relate: a computer program for maximum likelihood estimation of relatedness and relationship.
Molecular Ecology Notes 6:576-579.

BiolAD-DB 3.0.1 – Informatics System for Clinical and Genetic Data

BiolAD-DB 3.0.1

:: DESCRIPTION

The BiolAD-DB system is a research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password protected BiolAD-DB SQL compliant server database. BiolAD-DB tools further provide functionalities for generating customized reports and views.

::DEVELOPER

David Nielsen (email: nielsen@rockefeller.edu), Marty Leidner (email: marty@rockefeller.edu), Chad Haynes (email: haynesc@rockefeller.edu), Michael Krauthammer (email: michael.krauthammer@yale.edu), Mary Jeanne Kreek (email: kreek@rockefeller.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BiolAD-DB

:: MORE INFORMATION

Citation:

Nielsen, D.A., Leidner, M., Haynes, C., Krauthammer, M., and Kreek, M.J. (2006)
The BiolAD-DB System – An Informatics System for Clinical and Genetic Data.
Molecular Diagnosis & Therapy: 11, 15-19 (2007).

SelSim 2.1 – Simulate Population Genetic Data with Selection and Recombination

SelSim 2.1

:: DESCRIPTION

SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recombining region within which a single bi-allelic site has experienced natural selection. SelSim allows simulation from either a fully stochastic model of, or deterministic approximations to, natural selection within a coalescent framework. A number of different mutation models are available for simulating surrounding neutral variation. The package enables a detailed exploration of the effects of different models and strengths of selection on patterns of diversity.

::DEVELOPER

Chris C A Spencer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 SelSim

:: MORE INFORMATION

Citation

Spencer C., Coop, G. (2005)
SelSim: A program to simulate population genetic data with selection and recombination.
Bioinformatics. 2004 Dec 12;20(18):3673-5.

GDA 1.1 – Analyze Discrete Population Genetic Data

GDA 1.1

:: DESCRIPTION

GDA (Genetic Data Analysis) is a software for computing linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.

::DEVELOPER

Paul O. Lewis and Dmitri Zaykin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GDA

:: MORE INFORMATION

“Genetic Data Analysis” by Bruce S. Weir (1996, Sinaur Associates)