This tool finds the optimal rotation for a set of circular DNA sequences that are going to be aligned. It is very well suited to apply to mitochondrial genome alignments, and also for small plasmids, chloroplasts, circular viruses and bacterial chromosomes.
The best rotation is calculated based on the longest chain of non-repeated blocks that belongs to all the sequences simultaneously. These maximum common blocks are obtained with the help of a generalized cyclic suffix tree data structure.
As of yet, the current version of this tool does not perform the multiple sequence alignment itself. But other existing multiple sequence alignment tools can be used to perform this final task.
Use unzip to unpack and make to compile.
Run with:
./CSA R <multi-fasta-file>If you use CSA, please cite:
Please send your comments, suggestions, bug reports or questions to: