We present a new polynomial time approximation scheme (PTAS) for tree alignment, which is an important variant of multiple sequence alignment. As in the existing PTASs in the liter...
A progressive alignment algorithm produces a multi-alignment of a set of sequences by repeatedly aligning pairs of sequences and/or previously generated alignments. We describe a ...
We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of...
Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modi cation of sequen...
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements of genomes. To perform large comparisons efficiently, BLAST (Methods: Companio...