LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.
SiGN-SSM is open source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by the statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.
SiGN-L1 is network estimation software using sparse learning. It uses L1-regularization for simultaneous parameter estimation and model selection of statistical graphical models such as graphical Gaussian models and vector autoregressive models.
EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms
The micropower package is designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).
Phyto-PhyloPars web server takes an evolutionary perspective to the variability across phytoplankton taxa in order to estimate the size, maximum growth rate, phosphate affinity and susceptibility to predation of any phytoplankton taxon, based on over one thousand observations on freshwater species.
PhyloPars provides an efficient and statistically consistent method of combining any number of empirical observations with the phylogenetic tree to arrive at complete set of estimates for missing parameter values.
ReMixT is a tool for joint inference of clone specific segment and breakpoint copy number in whole genome sequencing data. The input for the tool is a set of segments, a set of breakpoints predicted from the sequencing data, and normal and tumour bam files. Where multiple tumour samples are available, they can be analyzed jointly for additional benefit.
The Data2Dynamics software package is a collection of numerical methods for quantitative dynamic modeling and a comprehensive model and data description language. The software facilitates the construction of dynamical models for biochemical reaction networks, but is not limited to this.
BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.