:: DESCRIPTION
SNV-PPILP is a fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny.
::DEVELOPER
GSA (Genome-scale algorithmics) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
SNV-PPILP: Refined SNV calling for tumor data using perfect phylogenies and ILP.
van Rens KE, Mäkinen V, Tomescu AI.
Bioinformatics. 2014 Nov 13. pii: btu755
:: 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
:: DOWNLOAD
:: 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.
