$ git clone https://github.com/weigelworld/minitv
$ python3 -m virtualenv .minitv-venv
$ source .minitv-venv/bin/activate
$ pip install minitv/
minimap2 must be in your PATH for minitv to run.
Either install it globally or download the binary from
the GitHub repository
and copy it into .minitv-venv/bin.
minitv --aligner_args "-x asm5 -g 150" --no_tree -a test_data/ACD6/TAIR10.gff3 -a test_data/ACD6/Col-0.gff3 -a test_data/ACD6/KBS-Mac-74.gff3 -a test_data/ACD6/Kn-0.gff3 -a test_data/ACD6/Ty-1.gff3 test_data/ACD6/TAIR10.fa test_data/ACD6/Col-0.fa test_data/ACD6/KBS-Mac-74.fa test_data/ACD6/Kn-0.fa test_data/ACD6/Ty-1.fa > out.alitv.json
The resulting out.alitv.json file can be loaded into any AliTV instance, such as
this demo site, by going to the "Import and Export" tab and clicking
the "Load JSON" button.