chromEvol_model_adequacy

Model adequacy for likelihood models of chromosome-number evolution. This framework uses simulations to assess whether a given model of chromosome-number evolution provides a realistic description of the evolutionary process.

Output:

Supplementary output files will be located in the output directory specified by the user. Model adequacy simulations together with final results will be located under /adequacy_test sub-directory. Output files include:

• In the output directory specified by the user:
  • tree_wo_counts.tree: phylogeny without coutns in the tips labels, based on the tree provided by the user.
  • tree_with_counts.tree: phylogeny with coutns in the tips labels, based on the tree provided by the user.
  • root_freq: root grequencies as extracted from the results file.
  • increasing_max_chr.txt: while simulating the upper bound was reached. Another iteration of simulations is running.
  • orig_stats: empirical test statistics calculations.
  • stats_dist_sims: the distributions of each statistics, over n simulations.
• A /simulations directory is also created, which contains:
  • param_sim: simulations parameters (as extracted from the results file).
  • log.txt: log file for simulations.
  • subdirectories contatining the simulations.

Prerequisites:

1. Python-3.6.5 or newer.
2. Python modules: os, argparse, re, ete3, scipy, numpy, subprocess.
3. R-3.5.1 or newer.
4. R packages: phytools, phangorn (version 2.7.0 and newer).
5. chromEvol: download chromEvol from chromEvol_model_adequacy repository located inside the chromEvol folder, for Linux. If you wish to run Model adequacy for chromEvol on Windows, download chromEvol source from here and follow the compilation instructions here.

Installation

1. Download all scripts of chromEvol model adequacy to the same directory.
2. Verify that you have the following paths or input files (see examples in the example directory):

• chromEvol executable path: chromevol_path = r"<YOUR_PATH>\chromevol.exe" (for exmplae: C:\Users\Downloads\chromevol.exe)
• R executable path: R_path = r"<YOUR_PATH>\Rscript.exe" (for example: C:\Program Files\R\R-3.6.2\bin\Rscript.exe)
• counts file in FASTA format
• phylogeny file in NEWICK format (the mlAncTree.tree inferred by chromEvol)
• chromEvol results file

Running

Modify paths to local executables (required)

In defs.py (definitions file) change the R_path and chromevol_path variables to your executable paths. Full paths are required. See Installation for examples.

The -c <full_path_to_counts_file> parameter: (required)

The empirical data the model in question was fitted to, given in a FASTA format.

The -t <full_path_to_tree_file> parameter: (required)

The inferred ancestral reconstruction phylogeny in a NEWICK format (by default, named mlAncestors.tree by chromEvol).

The -r <full_path_to_results_file> parameter: (required)

The chromEvol results file from which the simulating parameters will be extracted.

The -out <full_path_to_output_directory> parameter: (required)

The output directory to which all relevant output files, as well as the simulations and final results will be printed to. Note that in this directory supplementary files will be written, and the model adequacy test itself will be written to a subsequent /adequacy_test sub-directory.

The -n <number_of_simulations> parameter:

The number of simulations requested by the user. If not set by the user, the default is 1,000.

Runnign example:

This can be downloaded from the example folder.

python ~/main.py -c ~/example/counts -t ~/example/tree -r ~/example/chromEvol.res -out ~/example/ -n 1000