Installation

1. Create your virtual environment python3.9 -m virtualenv venv

2. Activate your virtual environment source venv/bin/activate

3. Follow the instructions at https://github.com/veg/hivtrace for installation

pip3 install biopython
pip3 install numpy==1.20
pip3 install scipy
pip3 install cython
pip3 install hivtrace

4. Ensure tn93 is installed

git clone https://github.com/veg/tn93.git
cd tn93
cmake .
make
make install (optional)

5. Run HIV-TRACE with Dummy Dataset HIV-TRACE currently only anticipates a FASTA file. A dataset used in an analysis in 2019 is available at https://github.com/veg/kpnet-global/blob/master/data/kp-aligned.fas.

The range we're using is

• Sites : 2253-3869
• Minimum Length : 500

hivtrace -i ./sequence.fasta -t 0.015 -r /Users/sweaver/Programming/hivtrace/hivtrace/test/rsrc/HXB2_1497.fasta -a resolve -m 500 -g 0.015

Documentation for hivtrace is located at https://github.com/veg/hivtrace.

hivnetworkannotate -n sequence.fasta.results.json -a attributes.json -g schema.json -r

Some documentation for for hivnetworkannotate exists at https://github.com/veg/hivclustering/wiki/hivnetworkannotate.

6. Visualize

https://veg.github.io/hivtrace-viz/

Prior Network Handling

• https://github.com/veg/hivclustering/blob/master/docs/incremental.md