Documentation
=============

See documentation in docs/index.html


Folder structure
================

bin/ contains the pnavsmna.jl file that should be used to calculate alignment quality scores

data/ contains network files used the the documentation

docs/ contains documentation for calculating alignment quality scores (docs/index.html contains the main documentation file and should be used as the starting point for exploring the rest of the documentation)

examples/ contains example files relevant to the documentation

git/ contains files used to install the PNA vs MNA software

install_pnavsmna.jl is the file that should be used to install the PNA vs MNA software, as explained in the documentation

src/ contains the alignment quality score calculation source files

utils/ contains files that is used to convert multiple alignments to pairwise alignments and vice versa
