About the LAGAN Toolkit
CHAOS
The LAGAN Tookit consists of four components:
CHAOS is a pairwise local aligner optimized for non-coding, and other poorly
conserved regions of the genome. It uses both exact matching and degenerate
seeds, and is able to find homology in the presence of gaps.
LAGAN
LAGAN is our highly parametrizable pairwise global alignment program. It takes
local alignments generated by CHAOS as anchors, and limits the search area
of the Needleman-Wunsch algorithm around these anchors;
Multi-LAGAN
Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence
alignment. M-LAGAN performs progressive pairwise alignments, guided by
a user-specified phylogenetic tree. Alignments are aligned to other alignments using
the sum-of-pairs metric.
Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions,
transpositions and some duplications) in a global alignment framework. It uses CHAOS local
alignments to build a map of the rearrangements between the sequences, and LAGAN to align the
regions of conserved synteny.
