Open Source Bio-Informatics Software

Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.

The primary driver of speciation may result from hybridization instead of the accumulation of mutations. The accumulation of mutations may instead be responsible for a "maturation" which may have real physical meaning rather than being an amorphous concept. Scientists such as Donald Williamson and Lynn Margulis have suggested similar ideas but perhaps not going as far as this project assumes. This software converted the Catalogue of Life, catalogueoflife.org, into a gedcom format. It no longer works due to the Catalogue's database format change. This present project extends the gedcom format for use in systematics or species categorization. All named taxonomic levels are assumed to have originally been individual species and the software/database outputs all species as female until hybridization events can be added manually. This tool is used to develop the data at http://genealogyoflife.com. It converted the data from 1.2 million species to over 2 million gedcom females.

Diktyologia is software for investigating complex systems with advanced methods of network theory. The package allows for analysing statistical properties of directed intercausal networks that are represented in form of cy.prus XML files.

Controversial ideas of Williamson, Margulis & others suggest speciation by hybridizing might be more common than originally thought. Taking this concept to the nth degree & assuming that indeed, speciation mostly occurs by hybridizing events, not the accumulation of mutations or genetic drift, here is a catalogueoflife2gedcom converter. It allows the tree of life to be displayed as a human genealogy tree with hybridizing events depicted as "marriages." The idea then is that mutation accrual & genetic drift are the determining factors for "species maturation," not speciation itself. Unfortunately the Catalogue of Life Project, catalogueoflife.org, changed its database format more recently, so this converter only works on older versions of the data. In the last working version of the database, making the assumption that each taxonomic name, no matter what level, refers to an original real species & starting them all as female, over 2 million "species/persons" were generated.

An interactive tool for the simulation and visualization of the electromagnetic activity of the brain.

A C# implementation of LOGO which allows to reproduce many real world (complex) phenomena governed by local rules like traffic jams, gas diffusion, aggregation and percolation, ant systems and biological systems in general.

TRiDaS is a universal data exchange standard for the dendrochronology community. This project contains the data standard itself as well as libraries and tools useful for reading, writing and converting dendro data files.

Simple console program intended for factor or principal components analysis. It calculates the optimal number of factors using the Horn's parallel analysis, computes the Kaiser-Meyer-Olkin and a few other measures of sampling adequacy.

Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.

RPowr is a simple calculator for planning correlational research. It computes the power of the Pearson correlation coefficient allowing adjustment for unreliability and range restriction of the variables (e.g. predictor and criterion measures).