Software accompaniment to
1. Yufeng Wu, "Close
lower and upper bounds for the minimum reticulate network of multiple
phylogenetic trees", in Proceedings of ISMB 2010, Bioinformatics 2010 26(12):i140-i148, 2010. Here is
the preprint of this paper PDF.
2. Yufeng Wu, "An Algorithm for Constructing Parsimonious
Hybridization Networks with Multiple Phylogenetic Trees", in
Proceedings of RECOMB 2013. Here is the preprint of the this paper PDF.
PIRN is a program for reconstructing the most parsimonious
phylogenetic networks that contain a
set of given phylogenetic trees. One motivation is that the trees are
the gene trees and the phylogenetic networks model what may have happen
when there is horizontal gene transfer. An example of phylogenetic
network produced by PIRN is shown above, which contains five input gene
trees (see the Appendix of my ISMB paper for these five trees). The
main functions of PIRN is computing a lower bound on the minimum
reticulation needed and also reconstructing a network that is usually
close to optimum.
1/8/2013: v2.0.1: This is a new code release. The main new
feature
is the ability of constructing the exact most parsimonious
hybridization network for multiple rooted binary trees. Note this works
only for relatively small number of reticulations (specified by -r
option). See the Readme file for more details.
Note: Files can be downloaded using "Save
Link/Target As..." After downloading the softwares, you may
need to change file access permissions (e.g. chmod u+x pirn).
Source code is available upon request .
Current version: v. 2.0.1. Source code
available (see below)
