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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller22 weekly downloads
Cloud storage class, open source software.
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Maximal Clique Motif Reduction (MCMR) is a software program for running and then combining the output of multiple motif finder programs, such as MEME, AlignACE and Weeder, into a set of consensus predictions with associated confidence rankings.
Cancer driver prediction via integrative omics5 weekly downloads
Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.12 weekly downloads
Code for reference implementations of identity brokers and simple single sign-on (SSO) mechanisms that utilize XDI and link contracts to manage the dataweb.
WideStudio is an Integrated Development Environment (IDE) for building window applications in C++, Ruby, Python an Perl for Windows, MacOSX, Linux, FreeBSD, SOLARIS and other unix and BTRON and T-Engine. This is open and free (under MIT/X Consortiun Lice47 weekly downloads
Support for the Oasis XRI (Extensible Resource Identifiers) effort. This includes resolvers and client libraries for XRIs in multiple languages and multiple platforms. See http://www.oasis-open.org/committees/xri2 weekly downloads