MetaPASSAGE, a software pipeline to generate in silico bacterial communities, simulates a sample of shotgun reads from a gene family represented in the community, orient or translate reads, and produce a profile-based alignment of the reads from which a gene-family phylogenetic tree can be built.
AEGIS is an open-source software with an interactive information-retrieval framework that enables an investigator to navigate through the entire Gene Ontology (GO) graph (with tens of thousands of nodes) and focus on fine-grained details without losing the context.
AlphaSimR is the successor to the AlphaSim software for breeding program simulation and a package for the R software environment. AlphaSimR builds on lessons learned from development of our previous software and the use of this software to perform simulations of breeding programs. The result is a software package this is both easy-to-use and flexible. This ease-of-use and flexibility provides users with the ability to simulate a wide range of complex plant and animal breeding programs.
GenomeSmasher is a set of tools used to create diploid FASTA files with containing snps, indels, duplications, deletions and translocations. These FASTA files can then be used in conjunction with next-generation sequencing simulators to artificially create sequencing experiments. The utility of these tools are to assess the performance and reliability of data analysis in next-generation sequencing pipelines.
gargammel is a set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.