Recombulator calculates the expected recombination frequency between any two loci on any chromosome of the fly genome, given as a gene name or a genomic coordinate. Recombination frequencies vary along all eukaryotic chromosomes, and these frequencies have been determined empirically with relatively high precision in the genome (Ashburner).
R. Suggested: Rstudio
The easiest way to run these functions is to open "Recombulator.Rmd" in Rstudio, and run all the chunks so that the example code renders. Look at the examples and code, and change the desired input values before rerunning the chunks. Once you understand the output graphs, it should be fairly obvious what you need to do.
Shiny web app (help!)
I originally wrote these functions in python as a Tkinter app, (original file date 1/27/2009). If anyone can help make these run again I would appreciate it greatly!! Here are the original README contents.
Recombulator is a suite of python functions that serve to calculate the recombination frequency between any two loci on any chromosome of the fly genome, given as a gene name or a genomic coordinate. The code has been tested on a python interpreter shell on a Debian Linux with AMD64/x86-64 in 32 bits and later in 64 bits on a dual core processor.
This directory contains two files that are necessary to run recombulator.
recombTools.py geneheader.txt
Tkinter, python-psyco (recommended)
To run recombulator in user-friendly mode, simply execute recombTools.py in python from the command line, and the GUI will appear.
If you have the python-psyco module installed you can uncomment the lines pertaining to psyco at the beginning of the program.
COPYRIGHT Dannis J. Hazelett. All code described herein is distributed under the GNU public license (GPL). A copy of the license (gpl-3.0.txt) is included in this directory, but can also be obtained from http://www.gnu.org/licenses/gpl.html.