Processes

The workflow has the following steps in it:

• Input fasta pairs are aligned to one another with muscle.
• Gap characters in aligned fasta are replaces with X character.
• The pairs are split into individual fasta files with faSplit byname tool.
• Each fasta for the pair is then fragmented using the pyfasta split where -k flag is used to define window size and -o flag is used to define overlap between fragments. -Fragmented files are then subjected to blastp.
• blastp output is then parsed to obtain a table of fragment to fragment match and percent identity shared by a pair of fragments.
• The window size vs percent ID plots are generated to visualise the breakpoints of diversification and recombination.