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A disordered collection of scripts to get some stats about core genes of S. pneumoniae
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.gitignore
LICENSE
README.md
aa_pis.txt
accessory_hyphy.pl
avg_aa_length.txt
avg_seq_length.pl
calc_pi.py
core_cls_names.xlsx
hyphy_array.pl
interactive_plot.R
parse_SLAC_json.pl
parse_site_SLAC_json.pl
run_hyphy.pl
run_hyphy_SLAC.pl
slac_results.txt

README.md

pneumo_core

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

See http://www.johnlees.me/blog/2019/04/17/conservation-of-core-genes-in-s-pneumoniae/

Details

A bit of a mess! Key scripts:

  • run_hyphy_SLAC.pl - Runs IQTREE and SLAC (using HyPhy).
  • parse_SLAC_json.pl – A terrible way to 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.
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