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PALS is obsolete and no longer supported.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.
LASTZ and PILER
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.
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
Reference
R.C. Edgar and E.W. Myers, PILER: identification and classification
of genomic repeats.
Bioinformatics.
2005 Jun 1;21 Suppl 1:i152-i158
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