To reproduce the graphs and trees, run each executable file in this directory in order. That is, do ./01_annotate.r, then ./02_crosscontam.sh, and so on. Any files which are not executable don't need to be run. 00_raw.csv is the data file which was initially provided by Conan.

Steps:

• 01_annotate.r: reshape the csv file to be easier to use in later steps
• 02_crosscontam.sh: find cross-contamination
• 03_figures.sh: create the frequency through time plots and fitness curve (using code from Art)
• 04_fasta.r: get patient data into FASTA format
• 05_align.sh: align nucleotide sequences with MAFFT
• 06_tree.sh: create trees for each patient with RAxML
• 07_pattrees.sh: draw one tree per patient with day 0 and 7 sequences