CTE Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination

Synopsis

This prototypic program is a implemenation of the approach described in the research paper

Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination

by Sebastian Will, Anke Busch, and Rolf Backofen

accepted by Constraints Journal, 2007.

It implements the inference-based constraint solving technique Cluster Tree Elimination for the solving of sequence alignment with side constraints.

CTE-Alignment is written by Sebastian Will, Copyright 2006-2007. Its released under GPL.

Download and Installation

CTE-Alignment is distributed as source [cte-alignment-0.8.tar.gz].

CTE-Alignment should run on recent Linux systems. Installation under Linux/Unix follows the usual scheme:

tar xzf cte-alignment-0.8.tar.gz
cd cte-alignment-0.8

./configure
make

Currently, please DO NOT install the program by
make install

Usage

In the same directory you may try the small examples by
cte-alignment < example-input
cte-alignment < example-input2