SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments. SAM aims to be a format that:

- Is flexible enough to store all the alignment information generated
  by various alignment programs
- Is simple enough to be easily generated by alignment programs or
  converted from existing alignment formats
- Is compact in file size
- Allows most of operations on the alignment to work on a stream
  without loading the whole alignment into memory
- Allows the file to be indexed by genomic position to efficiently
  retrieve all reads aligning to a locus. 

SAM Tools provide various utilities for manipulating alignments in the
SAM format, including sorting, merging, indexing and generating 
alignments in a per-position format.

NOTE!
This is an older version of the program, kept here for compatibility
with Ugene. You can safely install it along the new one. When you start
Ugene, go to Settings > Preferences > External Tools and manually select
the legacy binaries in /usr/bin/

Publication:
Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N.,
Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data
Processing Subgroup (2009) The Sequence alignment/map (SAM) format and
SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]