G-PhoCS - Generalized Phylogenetic Coalescent Sampler
G-PhoCS is a demography inference method based on analysis of individual genomes sequenced to high quality at thousands of
loosely linked, neutrally evolving loci. G-PhoCS receives as input a population phylogeny augmented by a set of migration bands,
with multiple sequence alignments from putative neutral loci along the genome. The method is fully Bayesian, producing a series of
values for the demographic parameters (population divergence times, effective population sizes, and migration rates)
sampled according to an approximate posterior distribution. G-PhoCS uses Markov Chain Monte Carlo (MCMC) to jointly sample
model parameters and genealogies at the input loci.
cite: Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43:1031-1034
See G-PhoCS website for latest version of code
INSIGHT - Inference of Natural Selection from Interspersed Genomically coHerent elemenTs
INSIGHT is a method for inferring the influence of natural selection on DNA sequences in many short
and interspersed genomic elements. The core of the method is a full probabilistic model that allows it to make use of
information on sequence polymorphism and divergence across a dispersed set of elements to disentangle the effects of
neutral genetic drift from positive, strong negative, and weak negative selection. It is specifically designed to analyze
short regulatory elements, such as the binding sites of transcription factors and microRNAs.
cite: Gronau I, Arbiza L, Mohammed J, Siepel A. (2013) Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence. Molecular Biology and Evolution 30(5):1159-1171
See INSIGHT website for latest version of code +
web server for submitting regions for remote analysis
