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.

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).