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Java implementation of global alignment using a variation of Levenshteindistance. It takes first two sequences from fasta file and returns aligned sequences also in fasta format.

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Java pairwise global alignment

(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.

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Java implementation of global alignment using a variation of Levenshteindistance. It takes first two sequences from fasta file and returns aligned sequences also in fasta format.

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