About PALS
PALS is public domain software that finds local alignments of long DNA sequences. PALS stands for Pairwise Aligner for Long Sequences. It was designed for use in our PILER package for genomic repeat analysis, but may also be useful in other applications.

Credits
PALS was written by Bob Edgar and Gene Myers.

Download
Click here to download. Source code only, 24 kb file, tarball (.tar.gz) format. 

Documentation
 Manual as a PDF file
Manual as a web page

Citing PALS
Please cite:

R.C. Edgar and E.W. Myers, PILER: identification and classification of genomic repeats.
Bioinformatics. 2005 Jun 1;21 Suppl 1:i152-i158

An important element of the algorithm is a technique for finding seed alignments that will be published in the following paper.

Rasmussen, K., Stoye, J. and Myers, E. (2005) Efficient q-gram filters for finding all e-matches over a given length. Proc. RECOMB 2005.

News and updates
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