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
Original software, written in Python.
- 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
- 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/.
Improved version with randomization, written in Java.
- For usage, see comments in file Pivo2.java