Welcome to IQPNNI - Important Quartet Puzzling and NNI Operation
Introduction:
An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic
tree based on DNA or amino acid sequence data. Our approach
combines various fast algorithms to generate a list of potential
candidate trees. The key ingredient is the definition of so-called
important quartets (IQs), which allow the computation of an
intermediate tree in O(n^2) time for n sequences. The
resulting tree is then further optimized by applying the
nearest neighbor interchange (NNI) operation. Subsequently a random
fraction of the sequences is deleted from the best tree found so far. The deleted
sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.
These steps are repeated several times and the best tree, with respect to the
likelihood criterion, is considered as the inferred phylogenetic
tree. Moreover, we suggest a rule, which indicates when to stop the search.
Latest version IQPNNI 3.3.1 (8th December 2008):
Important: A bug in the recent release 3.3 was identified that affects the bootstrap option. When user turns on the bootstrap, the bootstrap resampling is done before the random seed number is generated, making all bootstrap alignments
the same in all runs. We therefore strongly recommend you to download and install the bug fix release 3.3.1.
We are pleased to announce that IQPNNI 3.3 has come out with some important features like easier non-parametric bootstrap. It also fixed some important bugs from IQPNNI version 3.2. Therefore, we strongly recommend you to download and install this new version.
Please read the User Manual (or in PDF format) carefully before using IQPNNI the first time or when you upgrade the new version!
Download:
Source package and sequential binary releases for Linux, MacOS and Windows are available in gzipped TAR format and ZIP format. No binary
release for parallel version is available, you have to build it on your own machine.
In the all-in-one binary release you find all 32bit executables for Linux, MacOSX, and Windows, thus are compatible with 64bit OS. The binaries were complied with GCC 4.0.2 (Linux, MacOSX) and MinWG (Windows) and statically linked.
Older versions:
Go to Version History to find out more about the development of IQPNNI and for downloading older version releases.
Reference:
The method are described in details in the following articles:
- Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time. Mol. Biol. Evol., 21(8):1565-1571.
(free reprint,
DOI: 10.1093/molbev/msh176,
PMID: 15163768)
- Bui Quang Minh, Le Sy Vinh, Arndt von Haeseler and Heiko A. Schmidt (2005)
pIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics, 21(19):3794-6.
(free reprint,
DOI: 10.1093/bioinformatics/bti594,
PMID: 16046495)
- Bui Quang Minh, Le Sy Vinh, Heiko A. Schmidt, and Arndt von Haeseler (2006) Large Maximum Likelihood Trees.
Proceedings of the NIC Symposium 2006, 357-365, Forschungszentrum Jülich, Germany.
(ISBN 3-00-017351-X) NIC series (PDF)
Note:
- Please, let us know if you download this program by sending an email to {minh.bui,arndt.von.haeseler}@univie.ac.at
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