diCal 1.3 / diCal-IBD 1.0 – Predicts Identical by Descent Tracts using Sequence data

diCal 1.3 / diCal-IBD 1.0

:: DESCRIPTION

diCal is a scalable demographic inference method based on the sequentially Markov conditional sampling distribution framework.

diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing

::DEVELOPER

The Biophysics Graduate Group, Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  diCal-IBD , diCal

:: MORE INFORMATION

Citation

Genetics. 2013 Jul;194(3):647-62. doi: 10.1534/genetics.112.149096. Epub 2013 Apr 22.
Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.
Sheehan S1, Harris K, Song YS.

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.
Tataru P, Nirody JA, Song YS.
Bioinformatics. 2014 Aug 21. pii: btu563

IBDmap – Identical by Descent Mapping

IBDmap

:: DESCRIPTION

IBDmap is the factorial HMM based algorithm.Several models are supported in this implementation, including both the standard model and the 4-track model which uses a first order Markovian model for the LD process in a subset of the founders.

::DEVELOPER

Laboratory of Computational Biology at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 IBDmap

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i175-82. doi: 10.1093/bioinformatics/btq204.
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping.
Bercovici S, Meek C, Wexler Y, Geiger D.