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CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,...

This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE.

...I obtained AMPL from trial version of MOSEK at http://www.mosek.com/. CPLEX 12.0 can be obtained from http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/. A free acadamic license can be obtained by filling out IBM academic initiative application.

Perl Node Interface (PNI) is a node based visual programming environment. PNI makes easy to humans to write Perl programs. No Perl skill is required, programs are builded graphically. Perl coders can easily extend it writing new nodes.