SHAPEIT 4.2.1 – Accurate and Efficient Phasing of Genetic datasets

SHAPEIT 4.2.1

:: DESCRIPTION

SHAPEIT (Segmented HAPlotype Estimation and Imputation Tool) is a program for accurate and efficient phasing of genetic datasets

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 SHAPEIT

:: MORE INFORMATION

Citation

Delaneau O, Zagury JF, Robinson MR, Marchini JL, Dermitzakis ET.
Accurate, scalable and integrative haplotype estimation.
Nat Commun. 2019 Nov 28;10(1):5436. doi: 10.1038/s41467-019-13225-y. PMID: 31780650; PMCID: PMC6882857.

O. Delaneau, JF. Zagury, J. Marchini (2013)
Improved whole chromosome phasing for disease and population genetic studies.
Nature Methods  2013 Jan;10(1):5-6

Recomb – Simulate Genetic Datasets with Recombination Rates Changing Over Time

Recomb

:: DESCRIPTION

The program ms_recomb, a modified version of Richard Hudson’s ms, uses the coalescent to simulate genetic datasets with recombination rates that change through time.

The program msstats_recomb, an extensively modified version of Kevin Thornton’s msstats, implements n-tuple subsampling and calculates a suite of summary statistics with specific focus on recombination events

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  Recomb

:: MORE INFORMATION

Citation:

Cox, M.P., B.R. Holland, M.C. Wilkins and J. Schmid. 2013.
Reconstructing Past Changes in Locus-Specific Recombination Rates.
BMC Genet. 2013 Feb 25;14:11. doi: 10.1186/1471-2156-14-11.