The program fur takes as input a set of target genome sequences and a set of related genome sequences, the neighbors. It returns the sequence regions common to all targets that are absent form the neighbors. Such regions can be used as candidate genetic markers.

Bernhard Haubold, [email protected]

Make sure you've installed the packages git, golang, libdivsufsort-dev, make, ncbi-blast+, phylonium, primer3, and noweb. Then make the programs.
$ make
The directory bin now contains the binaries, scripts are in scripts.

As an alternative to building fur, we also post it as a docker container. The container includes all programs needed to work through the tutorial at the end of the documentation in ~/furDoc.pdf.

• $ docker pull haubold/fox
• $ docker run -it --env="DISPLAY" --net=host -v ~/fox_share:/home/jdoe/fox_share --detach-keys="ctrl-@" fox
  This constructs the directory fox_share in your home directory and in the container's home directory, for sharing files between the two environments.

Make sure you've installed the packages git, make, noweb, texlive-science, texlive-pstricks, texlive-latex-extra, and texlive-fonts-extra. Then make the documentation.
$ make doc
The documentation is now in doc/furDoc.pdf.

GNU General Public License