Open Source MinGW/MSYS2 Bio-Informatics Software

Critterding is a "Petri dish" universe in 3D that demonstrates evolving artificial life. Critters start out with completely random brains and bodies, but will automatically start evolving into something with much better survival skills.

Main application is twofold: first to convert genotype SNP data into formats of different imputation tools like PLINK MACH, IMPUTE, BEAGLE and BIMBBAM, second to transform imputed data into different file formats like PLINK, HAPLOVIEW, EIGENSOFT and SNPTEST. Readable file formats: plink-pedigree (ped and map), plink-raw, plink-dosage, mach , minimac, impute, snptest, beagle and bimbam. Similarly all kinds of imputation of outputs are also accepted. Formats which can be generated by fcGENE: plink-pedigree, plink-raw, plink-dosage, mach-inputs, minimac-inputs, impute-inputs, beagle-inputs and bimbam-inputs, HAPLOVIEW-inputs, EIGENSOFT-inputs. Further application: -obtaining templates of necessary imputation commands and commands of other imputation tool - Quality control according as MAF,HWE & CALLRATE. key words: genotype transformation, convert genotype format, imputation output, PLINK, IMPUTE, MACH, minimac, HAPLOVIEW, BEAGLE, BIMBAM,EIGENSOFT.

A program to model HapMap haplotypes in genetic association studies using tag SNP genotypes. Please visit http://www.ucd.ie/genepi/hapmixmap for more details.

starrynite is an image analysis tool for tracking fluorescently-labeled nuclei during C. elegans embryogenesis.

Latronix Regnum Arts - Open Source Faction is an open source and freeware developer for all sorts of goodies. Be it games or applications. This is the home for the Drug Turfs Game (A Drug Wars like game) and the Drug Turfs Library.

NMR-Ghost a tool for analyisis and visualization of in-vivo NMR spectroscopic data

RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings.

Software for the visualization, analysis, and scoring of electrophysiological data.

ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing.

A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.

bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file for rapid extraction of subsets of the data. In theory bint could be used for any large tables of float data.

We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces.

The set of tools for biopolymer sequence analysis together with GUI to work with biopolymer sequence databases. The tools include pairwise and multiple alignment, philogenetic tree construction and other.