PIIM: Population Inference In Metagenomics

This program calculates maximum likelihood estimates of θ=2Nu (where u is the per-site mutation rate) and R=Nr (where r is the exponential growth rate) from metagenomic-style data (i.e. genome-level population data of variable sample depth and quality). For details on the method, see: Johnson, PLF and Slatkin M. 2006. "Inference of population genetic parameters in metagenomics: a clean look at messy data." Genome Research 16, 1320-1327.

Documentation (included with below)11kreadme.html
Source code w/ Makefile25kpiim.tar.gz
Linux binary277kpiim.i686.fedora4.tar.gz
Sludge data (analyzed in paper)4msludge.tar.gz

Note the sludge data comes courtesy of the Joint Genome Institute (JGI). This package contains the single largest contig (sludgePhrap_Contig16370) from the JGI's PHRAP assembly of the US sludge (see IMG/M for the full assembly).

last modified: 6 Aug 2007