Code accompanying LEISR manuscript
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empirical_analysis
figures
simulation_analysis
.gitignore
README.md
install_R_requirements.R
requirements.txt
test1e5.fna
test1e5.fna.site-rates.json

README.md

LEISR validation

This repository accompanies the manuscript Relative evolutionary rate inference in HyPhy with LEISR by SJ Spielman* and SLK Pond, currently in press at PeerJ.

Please see the "Publication Release" under the releases tab for the version of this repository that accompanies the published manuscript.

Dependencies

  • requirements.txt may be used to install all Python dependencies with the code pip install -r requirements.txt (with a prepended sudo as needed), called from this directory.

  • The script install_R_requirements.R can be run with Rscript install_R_requirements.R to install all R dependencies.

  • HyPhy version >= 2.3.8 and Rate4Site must be installed and available in your system path.

Repository contents

  • simulation_analysis contains code and data to reproduce simulations and subsequent inference, visualization

    • The Python script simulate_compare_methods.py performs all simulations and inferences.
      • Dependencies: pyvolve, phyphy
    • The R script process_and_plot.R processes rate inferences and makes figures that appear in MS
      • Dependencies: tidyverse, cowplot, broom
    • simulations_rates directory contains all simulated data and rate inferences. Note that trees used for simulation were generated with the ape R package and are saved in the files rtree<25,50,100.tre>.
  • empirical_analysis contains code and data to reproduce inference and visualization on empirical dataset. See README.md within the directory for details.

  • test1e5.fna and test1e5.fna.site-rates.json are a simulated (nucleotide) alignment of 10,000 sequences, with 100 sites, which is confirmed to run in LEISR (as indicated in MS).

*Please contact stephanie.spielman<at>temple.edu with questions.