https://github.com/kullrich/dagchainer
Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer
https://github.com/kullrich/dagchainer
dagchainer
Last synced: 6 months ago
JSON representation
Fork of the DAGchainer project https://sourceforge.net/projects/dagchainer
- Host: GitHub
- URL: https://github.com/kullrich/dagchainer
- Owner: kullrich
- License: mit
- Created: 2020-11-09T15:27:08.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2021-06-10T20:29:02.000Z (about 5 years ago)
- Last Synced: 2025-04-07T14:51:16.792Z (over 1 year ago)
- Topics: dagchainer
- Language: Roff
- Homepage:
- Size: 4.73 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://doi.org/10.5281/zenodo.4273760)
[](https://conda.anaconda.org/bioconda)
[](https://anaconda.org/bioconda/dagchainer)
# 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](https://sourceforge.net/u/jorvis/)
[Brian Haas](https://sourceforge.net/u/bhaas/)
Original Project Page:
[http://dagchainer.sourceforge.net/](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/](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](https://doi.org/10.1093/bioinformatics/bth397)