SILP2 – ILP-based Maximum Likelihood Genome Scaffolding

SILP2

:: DESCRIPTION

SILP2 is a stand-alone scaffolding tool that generates maximum likelihood scaffolds via integer linear programming (ILP). SILP2 achieves high scalability without sacrificing optimality by solving the large ILP formulations required to scaffold mammalian-size genomes via a non-serial dynamic programming (NSDP) approach based on decomposing the scaffolding graph into 3-connected components.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SILP2

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014;15 Suppl 9:S9. doi: 10.1186/1471-2105-15-S9-S9. Epub 2014 Sep 10.
ILP-based maximum likelihood genome scaffolding.
Lindsay J, Salooti H, Măndoiu I, Zelikovsky A.