dagchainer

Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer

DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).

Original Project Admins:

Joshua Orvis

Brian Haas

Original Project Page:

http://dagchainer.sourceforge.net/

only minor changes made to compile on macOS

Building DAGchainer

git clone https://github.com/kullrich/dagchainer.git
export PREFIX="."
cd dagchainer;make clean;make

Building DAGchainer - Bioconda

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

conda install dagchainer

Run DAGchainer

./dagchainer/bin/run_DAG_chainer.pl

Run Java_XY_plotter

./dagchainer/src/Java_XY_plotter/run_XYplot.pl ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered

Example

./dagchainer/bin/run_DAG_chainer.pl -i ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered -s -I
less ./dagchainer/src/data_sets/Arabidopsis/Arabidopsis.Release5.matchList.filtered.aligncoords

Manual

see manual and further options here http://dagchainer.sourceforge.net/

References

Haas B. J., Delcher A. L., Wortman J. R., and Salzberg S. L. (2004). DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics, 20(18), 3643-3646. https://doi.org/10.1093/bioinformatics/bth397