Maximum number of conflicts in phylogenetic trees

Oliver Eulenstein, Anastasia Halfpap, Bernard Lidický, Sydney Miyasaki, Florian Pfender, Jan Volec

This page is containing computer assisted parts of the paper titled Maximum number of conflicts in phylogenetic trees A preliminary version of the paper can be downloaded here.

You can download the technical things as one archive

• anc_M.zip (30MB)

Description of the files in anc_M.zip Below is old copy.

• rounding_Integer.sage ... SageMath tools for rounding semidefinite program
• rounding_exact.sage ... SageMath tools for rounding semidefinite program
• Makefile ... for building the program creating semidefinite program
• F_edges*__forbidden.txt ... list of forbidden (induced) subgraphs
• F_edges*__nX_labeled.txt ... list of labeled graphs on X vertices used in the calculation (generated)
• F_edges*__nX_unlabeled.txt ... list of all graphs on up to X vertices (generated)
• F_edges*__objective*.txt ... Function to optimize
• SDP_nX_?B_F_*edges*__objective.txt.dat-s ... semidefinite program - input to csdp(generated)
• SDP_nX_?B_F_*edges*__objective.txt.dat-s.result ... numerical solution from csdp (generated)
• SDP_nX_?B_F_*edges*__objective.txt.dat-s.result.rounded.... ... rational solution from numerical one by SageMath (generated)
• SDP_nX_LB_F_*edges*__objective.txt.dat-s.csdp.log ... csdp solver output (generated)
• round* ... scrips and outputs for rounding the semidefinite program.