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.
-
requirements.txt
may be used to install all Python dependencies with the codepip install -r requirements.txt
(with a prependedsudo
as needed), called from this directory. -
The script
install_R_requirements.R
can be run withRscript install_R_requirements.R
to install all R dependencies. -
HyPhy
version >= 2.3.8 andRate4Site
must be installed and available in your system path.
-
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
- Dependencies:
- The R script
process_and_plot.R
processes rate inferences and makes figures that appear in MS- Dependencies:
tidyverse
,cowplot
,broom
- Dependencies:
simulations_rates
directory contains all simulated data and rate inferences. Note that trees used for simulation were generated with theape
R package and are saved in the filesrtree<25,50,100.tre>
.
- The Python script
-
empirical_analysis
contains code and data to reproduce inference and visualization on empirical dataset. SeeREADME.md
within the directory for details. -
test1e5.fna
andtest1e5.fna.site-rates.json
are a simulated (nucleotide) alignment of 10,000 sequences, with 100 sites, which is confirmed to run inLEISR
(as indicated in MS).
*Please contact spielman<at>rowan.edu
with questions.