Contact:
- liu.yi.pei@gmail.com
- jonilaserson@gmail.com Reference:
- http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003754
- https://stacks.stanford.edu/file/druid:xp796hy4748/thesis-augmented.pdf
- Examine
Fire/sample_driver_script.m - Update
Fire/sample_driver_script.mwith correct paths to the location of theimmunitree_phylo directory - Update
Fire/sample_driver_scriptwith correct paths to the locations of the input files - Make sure that the chain type parameter (0 for heavy, 1 for light) is correct provided to the call to
pipeline_for_hiv.m - Examine the
.../Fire/output/* folder for output *.txtfiles: descriptions of the trees for parsing (There are 3 txt files per tree)- The three txt files corresponds to three perspectives of the tree: overall, per-node, and, per-read
- There are also png files to visualize the trees. The colorings correspond to the number of mutations from the assigned node