QC scripts for alignments
###missingness.py This script takes a fasta alignment as input and calculates the number of gaps/missing sites (denoted by "-") for each strain in the alignment and outputs this info in a file and a histogram.
Usage: missingness.py -i [inputfile]
###gapPositions.py This script takes a fasta alignment as input and calculates the number of gaps at each site in the alignment and outputs this to a file.
Usage: gapPositions.py [alignment]