Fitchi – Haplotype Genealogy Graphs based on Fitch Distances

Fitchi

:: DESCRIPTION

Fitchi is a python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics.

::DEVELOPER

EVOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Fitchi

:: MORE INFORMATION

Citation

Fitchi: Haplotype genealogy graphs based on the Fitch algorithm.
Matschiner M.
Bioinformatics. 2015 Dec 9. pii: btv717.

Pedigree-Draw 6 – Genealogy Visualization

Pedigree-Draw 6

:: DESCRIPTION

Pedigree-Draw is a software that provides for creation, editing and drawing of pedigrees, or family trees, of human or non-human extended family lineages. It was developed originally for use in analyzing population data gathered for biomedical and genetic research. Although not designed as a genealogical database per se, the program can be used to collect and edit biographical data found in the course of family history research, as well as pictures of family members, and display or print those data in hierarchical diagrams suitable for publication. Output may also be saved in Portable Document Format (PDF) for distribution via the Internet, or posting on websites.

::DEVELOPER

Jurek Software

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

  Pedigree-Draw

:: MORE INFORMATION

Margarita – Infer Genealogies from Population Genotype data

Margarita

:: DESCRIPTION

Margarita infers genealogies from population genotype data and uses these to map disease loci.

::DEVELOPER

Richard Durbin.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Margarita

:: MORE INFORMATION

Citation

Mapping trait loci by use of inferred ancestral recombination graphs.
Minichiello MJ and Durbin R
American journal of human genetics2006;79;5;910-22

sampletrees 20151127 / Rsampletrees 1.0.3 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.3

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 sampletrees / Rsampletrees 

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.