The ChromoGGL programs are designed for solving the following tasks:
- Computation of the distance between the two given chromosome structures
and finding a sequence of operations with the minimum total weight (distance)
that transforms one structure into another.
- Computation of the matrix of pairwise distances for the given set
of structures and generation of the tree, that matches the matrix best.
- The reconstruction of the structures on the evolutionary tree defined
by the structures at its leaves, usually from the section 2, not necessarily binary,
on the ancestral nodes of the tree; all structures can include paralogs.