RF-Net 2

Java software for computation of Robinson-Foulds Reticulation Networks

  • Software on the flu-crew github page: RF-Net 2
  • Contact: Alexey Markin (amarkin (at) iastate (dot) edu)

PDC-Median

Joint Cophenetic and Path-Difference median tree software

  • Software package (java): pdc-median.zip
  • README: README-pdc-median.pdf
  • Contact: Alexey Markin (amarkin (at) iastate (dot) edu)
  • This software package combines the algorithms presented in the following manuscrips:
    • Cophenetic Median Trees;
    • Efficient Local Search for Euclidean Path-Difference Median Trees;
    • Computing Manhattan Path-Difference Median Trees: a Practical Local Search Approach
    published in IEEE/ACM Transactioncs on Computational Biology and Bioinformatics.