Population dynamics software tools | Mathematical modeling

Implements the demographic model for the EA population of Tennessen et al. TennessenEAonly was used in a study that explores the impact of genetic model and population growth on distribution of genetic variance across the allele frequency spectrum underlying risk for a complex disease. This package has been implemented in Python and is available for local use.

Allows users to study microbial communities. DEMIC can infer the relative distances of contigs from the replication origin and compare bacterial growth rates between samples. It was used to estimate the growth rates in over 120 species-experiment combinations. This tool performs growth estimation based on principal component analysis (PCA) of contig coverages in multiple samples.

Performs models definition, simulators and formats. pLinguaCore is a library designed for cell-like, tissue-like and spiking neural-like P system simulators. The software provides several services, including parsers for input files and built-in simulators for cell-like P systems. It intends to cover as many variants of P systems as possible. pLinguaCore includes a built-in simulator for tissue P systems with cell separation rules.

Allows users to model, simulate and analyze complex, heterogeneous and multi-scale systems like a cell. E-Cell is a generic software package for cell simulation, based on structured Substance–Reactor Model (SRM), an object-oriented modeling theory. The software accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature. It includes ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm.

Permits to automate the selection of a partitioning scheme given a set of user-defined data blocks as input. PartitionFinder can be used to compare millions of partitioning schemes in a single run and to select good and often optimal partitioning schemes for a large range of DNA data sets. It was developed to simplify the selection of partitioning schemes and lead to concomitant improvements in phylogenetic analyses.