SyMAP (
Synteny
Mapping and
Analysis
Program) is a software package for
detecting, displaying, and querying syntenic relationships between sequenced genomes.

It is designed for medium-to-high divergent eukaryotic genomes (not bacteria).

It can align a draft genome to a fully sequenced genome
(see
peach), but not draft-to-draft.

It can perform self-synteny. It can align to FPC physical maps.
Latest SyMAP release: v5.1.1 (31-July-2022), see Release Notes.
This release has transferred the tarball download and the documentation to github.com.
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This project was partially supported by the National Research Initiative of USDA's National
Institute of Food and Agriculture, grant #0214643.
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All upgrades starting with release 7-Nov-2016 have been developed by CAS without funding.
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References
C. Soderlund, M. Bomhoff, and W. Nelson (2011) SyMAP v3.4: a turnkey synteny system with
application to plant genomes Nucleic Acids Research 39(10):e68
Link
C. Soderlund, W. Nelson, A. Shoemaker and A. Paterson (2006) SyMAP: A system for
discovering and viewing syntenic regions of FPC maps. Genome Research 16:1159-1168.
Link