MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the internal nodes of the phylogenetic tree. Since version 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes to have different gene content.
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).
ILP-WGD-Reconstructor is a unified ILP framework for core ancestral genome reconstruction problems. Genome rearrangements and whole genome duplications are considered. ILP-WGD-Reconstructor may solve general, restricted, and conserved versions of genome median problem and guided genome halving problem. It also may find double distance between two given genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes.