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The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in...

MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run.

Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).

NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the...

Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.