Ancestral Reconstruction Pipeline

• Images from hackathon
• Notes on pipeline details

Plan for refactoring

1. GetGenomes: remove config file, add option to specify output dir for output files
   1. -d<directory of input synmap files>

• • -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
  • -w w1,w2,w3,w4 <list of comma separated syntenic depths for genomes -- note these are paired ordered data with the -g option?>
  • -s < subgenome_file>
  • -o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files>
• MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for
  • -i <input file or directory>
    • File type is a set of vertex vertex weight
    • note: if directory, will batch process all files
  • -o <outfile or directory>