A Tree-Based Method of Sequence Alignment
In "The method description"
we present an original fast algorithm of sequence alignment and its
computer realization. There and in "An application example"
we provide several examples of the multiple alignement of regions upstream
the same gene in different genomes. An alignment is constructed with
the algorithm, which uses a binary tree representation of distances
between any pair of sequences from corresponding genomes (organisms).
If the binary tree is unknown, it is inferred by resolving all non-binary
nodes in a given non-binary tree, which is usually known. Thus, the algorithm
realizes fast generation of binary trees compatible with a given non-binary
tree and produces the best alignment by sampling the generated tree
space. The algorithm was tested with biological data and simulations.
An application example
The method description (PDF)
The program with a brief description