README.md

subproblem_solutions

Requires that otcetera tools be in your PATH.

The artifacts are solutions to subproblems in the subproblems/ directory:

• ott#####-solution.tre: A newick tree file containing a solution to the subproblem in subproblems/ott#####.tre

Produced by otc-solve-subproblem. Each subproblem is read separately (subproblems/ott#######.tre).

Here is some shell code to perform this:

   for i in ../subproblems/*.tre ; do
       n=$(basename $i)
       id=${n%.tre}
       otc-solve-subproblem $i -n${id} > ${id}-solution.tre
   done

Here the -n argument specifies the name of the root node. The correct name for this node can be extracted from the name of the subproblem file, as in the script above.

Also see documentation for otc-solve-subproblem in otcetera/README.md.