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.
2/19/2014: A related program called PIRNS is now published. It is related to
PIRN but often works faster for larger number of trees.
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.
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.
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)
