PIVO: Phylogeny by IteratiVe Optimization
A Practical Algorithm for Ancestral Rearrangement Reconstruction

This page contains supplementary material to our papers:

The Hemiascomycetes mtDNA Dataset

The Campanulaceae cpDNA Dataset

PIVO software

Original software, written in Python.

  • Pivo
  • run python genr.py T G n to generate n histories starting from a random one; T is a file with the input tree, G is a file with the input genomes; histories are generated into directory m
  • python genm.py T G n p works similarly, but every p-th history it starts with a history similar to the currently best history in m/.

PIVO2 software

Improved version with randomization, written in Java.

  • Pivo2
  • For usage, see comments in file Pivo2.java