TransPhylo 1.0 – Inference of Pathogen Transmission Tree given Phylogeny

TransPhylo 1.0

:: DESCRIPTION

TransPhylo is a software package for the Bayesian inference of infectious disease transmission from a phylogeny.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 TransPhylo

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.
Bayesian inference of infectious disease transmission from whole-genome sequence data.
Didelot X, Gardy J, Colijn C

ET-TDT – Evolutionary Tree-Transmission Disequilibrium Test

ET-TDT

:: DESCRIPTION

ET-TDT is a procedure to combine the benefits of measured haplotype analysis with TDT to find which haplotypes or groups of haplotypes, as defined in an evolutionary tree, are responsible for increased (or decreased) relative risk for a genetic condition.

::DEVELOPER

COMPUTATIONAL GENETICS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ET-TDT

:: MORE INFORMATION

Citation:

Howard Seltman, Kathryn Roeder, and B. Devlin,
Transmission/Disequilibrium Test Meets Measured Haplotype Analysis: Family-Based Association Analysis Guided by Evolution of Haplotypes
Am. J. Hum. Genet., 68:1250-1263, 2001

TADA 20140624 – Transmission And De novo Association test

TADA 20140624

:: DESCRIPTION

TADA is a novel statistical method that utilizes inherited variation transmitted to affected offspring in conjunction with (de novo) mutations to identify risk genes.

::DEVELOPER

COMPUTATIONAL GENETICS LAB At the UNIVERSITY OF PITTSBURGH MEDICAL CENTER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package

:: DOWNLOAD

 TADA

:: MORE INFORMATION

Citation

PLoS Genet. 2013 Aug;9(8):e1003671. doi: 10.1371/journal.pgen.1003671.
Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.
He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.