STDR - Spectral Top Down Reconstruction

Code for the paper "Spectral Top-Down Recovery of Latent Tree Models" (https://arxiv.org/abs/2102.13276)

Installing

You should install the package using pip. cd inside the stdr folder and run

pip install .

Now if you want to import the spectraltree package, for example for an experiment, you can simply run

import spectraltree

Testing

To run the test suite, cd to stdr and run

python -m unittest discover

To run a specific module:

python -m unittest tests.test_stdr

Installing RAxML

In order to use RAxML (A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". In Bioinformatics, 2014), the RAxML executible should be placed in spectraltree\libs\raxmlHPC_bin
For macOS the file should be named: raxmlHPC-macOS For Windows the file should be named: raxmlHPC-SSE3.exe For Linux the file should be named: raxmlHPC-SSE3-linux

For further details, look in spectraltree\raxml_reconstruction.py and https://cme.h-its.org/exelixis/web/software/raxml/

Documentation

Run

python setup.py build_sphinx

(You can also go into the docs folder and run make html). Then open docs/_build/html/index.html in a browser.