pneumo_core

A disordered collection of scripts to get some stats about core genes of S. pneumoniae

Details

Key scripts:

run_hyphy_SLAC.pl - Runs IQTREE and SLAC (using HyPhy).
parse_SLAC_json.pl – Parse the output from the above and extract the global dN/dS.
calc_pi.py - Calculates the pi values.
interactive_plot.R - Creates the table and plot from the blog.

Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
aa_pis.txt		aa_pis.txt
accessory_hyphy.pl		accessory_hyphy.pl
avg_aa_length.txt		avg_aa_length.txt
avg_seq_length.pl		avg_seq_length.pl
calc_pi.py		calc_pi.py
core_cls_names.xlsx		core_cls_names.xlsx
hyphy_array.pl		hyphy_array.pl
interactive_plot.R		interactive_plot.R
parse_SLAC_json.pl		parse_SLAC_json.pl
parse_site_SLAC_json.pl		parse_site_SLAC_json.pl
run_hyphy.pl		run_hyphy.pl
run_hyphy_SLAC.pl		run_hyphy_SLAC.pl
slac_results.txt		slac_results.txt