Quick start
After installing using one of the options mentioned in Quick Install, you're ready to run ROADIES! To get started:
Step 1: Download the test dataset (11 Drosophila genomes):**
mkdir -p test/test_data && cat test/input_genome_links.txt | xargs -I {} sh -c 'wget -O test/test_data/$(basename {}) {}'
This will save the datasets on a separate test/test_data
folder within the repository
Step 2: Run the pipeline
Note
ROADIES by default runs multiple iterations for generating highly accurate trees. For quick testing, use --noconverge
to run a single iteration.
Step 3: Analyze Output:
- Final UNROOTED newick tree saved as
roadies.nwk
in a separateoutput_files
folder. - Intermediate files (if
--noconverge
not used) saved in a separateconverge_files
folder.
Note
ROADIES outputs unrooted trees by default. You can reroot trees on your own or use the provided reroot.py
script in workflow/scripts/
(given a reference rooted species tree as input).