CastNet: a systems-level sequence evolution simulator.

ABSTRACT:

Background

Simulating DNA evolution has been done through coevolution-agnostic probabilistic frameworks for the past 3 decades. The most common implementation is by using the converse of the probabilistic approach used to infer phylogenies which, in the simplest form, simulates a single sequence at a time. However, biological systems are multi-genic, and gene products can affect each other's evolutionary paths through coevolution. These crucial evolutionary dynamics still remain to be simulated, and we believe that modelling them can lead to profound insights for comparative genomics.

Results

Here we present CastNet, a genome evolution simulator that assumes each genome is a collection of genes with constantly evolving regulatory interactions in between them. The regulatory

SUBMITTER: Rivera-Rivera CJ 

PROVIDER: S-EPMC10259028 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature