Tag: Hypothese

MultiOrigin 1.0 – Exploring Hypotheses about the number of origins and the time of origin of a species founded by discrete events

MultiOrigin 1.0

:: DESCRIPTION

MultiOrigin explores hypotheses about the number of origins and time of origin of species that are founded from an ancestral species through discrete events (i.e. polyploid species). The program uses a population divergence coalescence model together with a rejection sampling algorithm.

::DEVELOPER

Jakobsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows 

:: DOWNLOAD

  MultiOrigin

:: MORE INFORMATION

Citation

Jakobsson et al. (2006)
A Unique Recent Origin of the Allotetraploid Species Arabidopsis suecica: Evidence from Nuclear DNA Markers
Mol. Biol. Evol. 23: 1217-1231,

EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution

EvolSimulator 2.1.0

:: DESCRIPTION

EvolSimulator is a program that allows the simulation of evolution at the level of genes, gene families, and whole genomes. It was designed with the goal of investigating evolutionary phenomena like biased mutation regimes in different lineages, complicated patterns of selective pressure across sequences, and the confounding effects of paralogy and lateral genetic transfer.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 EvolSimulator

:: MORE INFORMATION

Citation

Beiko, R.G. and Charlebois, R.L. (2007).
A simulation test bed for hypotheses of genome evolution.
Bioinformatics 23:825-831.

SLIM 1.1 – Sliding Linear Model for Estimating the Proportion of true null Hypotheses in Datasets

SLIM 1.1

:: DESCRIPTION

SLIM (Sliding Linear Model) is a software to more reliably estimate π(0) under dependence. When tested on a number of simulation datasets with varying data dependence structures and on microarray data, SLIM was found to be robust in estimating π(0) against dependence. The accuracy of its π(0) estimation suggests that SLIM can be used as a stand-alone tool for prediction of significant tests.

::DEVELOPER

 the Tsai lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
:: DOWNLOAD

 SLIM

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):225-31. Epub 2010 Nov 18.
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.
Wang HQ, Tuominen LK, Tsai CJ.