(c) 2005 by Jakub Pas
- Java implementation of global alignment using a variation of Levenshtein[1] distance
- Rewritten to Java
- It takes first two sequences from fasta[2] file (one sequence per line) and returns aligned sequences also in fasta format.
##Usage:
javac *.java
java -cp . Main alignment.fas
Or create jar file:
javac *.java
jar cvfm alignment.jar manifest.txt *.class
java -jar alignment.jar alignment.fas
[1] Levenshtein, Vladimir I (1965). Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady. 10 (8): 707–710.
[2] Pearson W.R. and Lipman D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85(8): 2444-2448.