"Beehive" is designed to reconstruct tumor evolutionary history based on somatic mutations. The ploidy for each chromosome and tumor purity have to be inferred prior to using this tool. Beehive can also help to validate the inferred purity and ploidy. Click here to download and here to learn more.
"Meerkat" is a computational tool to identify genomic rearrangements from high-throughput sequencing data. It uses multiple clusters of discordant reads to identify more complex rearrangements than available methods and uses split-reads to ensure high accuracy, followed by analysis of sequence homology at the breakpoints. The mechanisms forming these rearrangements can be inferred based on the features of breakpoints. Click here or here to download the software package. Click here to download a demo dataset. Click here to learn more.