Open Source Unix Shell Bio-Informatics Software for Windows

MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy. Please, check out the most recent updates of the source code with the Github repository of MToolBox: https://github.com/mitoNGS/MToolBox or visit the Web version of MToolBox @ MSeqDR: https://mseqdr.org/mtoolbox.php

BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.

Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. Please visit the Cloudomics, project for cloud-based resources: https://sourceforge.net/projects/cloudomics-for-aws/

Fast Neurite Tracer (FNT) is a tool for semi-automated neurite tracing. FNT can handle big imaging data such as fMOST data. It can also process other types of light imaging data in general. FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data.

A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.

HitKeeper is a database application for use in BioInformatics. It deals with "hits" (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

(OBSOLETE) trace_utils is a program for processing sequencing trace data. The main goal of this program is to provide a completely free software in detecting SNPs like what polyphred has done, but with even higher accuracy and more flexibility.

TrimAl is a bioinformatic tool that cleans multiple protein or nucleotide sequence alignment. The clean alignment (as a result of the TrimAl cleaning process) is used for phylogenetic reconstruction. TrimAl improves the quality of the reconstructed trees

Simulation of allele-specific RNA-seq data