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.

PALS is obsolete and no longer supported.
At the time PILER was developed, there were no tools suitable for making local self-alignments of whole chromosomes or whole genomes. PALS was a quick hack to make local alignments for PILER. The code has significant limitations, e.g. the code is built for a 32-bit processor architecture and does not scale well to larger genomes. It would require a major effort to develop a new version. I now recommend using LASTZ for whole-genome self-alignments.

To replace PALS with LASTZ, you will need to set appropriate alignment parameters and convert hits to PILER-compatible GFF format. I haven't tried doing this myself, so unfortunately I can't offer advice on the best way to do this. If you implement a solution, please email me and I'll post your feedback here to help other users.

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

Manual as a PDF file
Manual as a web page

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