Open Source Python Bio-Informatics Software - Page 15

Yfitter is a program for assigning Y chromosome haplogroups to individuals sequenced at low coverage. It is designed to be used in a samtools/bcftools pipeline. Yfitter also supports haplogrouping using chip genotype data.

Inter University Multi-Modal Imaging

The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. The YMAP pipeline automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other categories of data and other pathogen species with small genomes.

Zherlock has now changed name to SciCraft and no longer hosted on sourceforge. Visit our new site at http://www.scicraft.org

alignlib is a C++ library for computing and manipulating sequence alignments of protein sequences. Most of the functions and classes are exported to python thus permitting easy scripting of complex tasks. Alignlib has moved to github (https://github.com/AndreasHeger/alignlib)

The aim of our programm is to help lab on counting species and analyze the results with statistics tools.

polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences

A set of bioinformatics tools for the open source bio-informatics platform "birch"

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

A lightweight python LIMS system

A web-based repository of plasmids and biobricks (see http://parts.mit.edu) plus related utility programs that support synthetic biology research. Note: This project is not updated any longer. A completely re-written and much better version of this web server can be found here: http://www.rotmic.org

NOW HOSTED ON GITHUB: https://github.com/kylebittinger/brocc Old releases are kept here for archival purposes.

Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file.

Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file.

HMM based algorithm for dna generation from peptides.

This project seeks to integrate knowledge, methods and data from various disciplines through the design and implementation of a system that allows for communications between languages and different platforms.

It is a Cross Language Interface Platform that allows different languages to call and execute functions of other languages using xml-rpc as the remote procedure call vehicle.

defunct

defunct

diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing

This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.

Find and analyze barcodes in DNA sequence files

Application to optimize DNA sequences coding protein to put in in the different organizm (f.e. human protein in E.Coli). It proposes the optimal cutting places to connect many shorter fragments into bigger one using ligaze.

This is a pure Python CGI-based implementation of a taxonomically intelligent species search engine. It searches biological databases for a taxonomic name. The search is done "on the fly" using web services (SOAP/XML) or URL API's.

Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.