The papers below address methodological issues in phylogenetics and ecological networks. Programs to implement some of the methods we have developed can be downloaded from this page.
PHYLOGENETIC STRUCTURE OF SPECIALIZATION: PSS
Pardo-De la Hoz, C. J., Medeiros, I. D., Gibert, J. P., Chagnon, P.-L., Magain, N., Miadlikowska, J., Lutzoni, F. 2022. Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks. Ecology and Evolution 12:e8649.
GitHub repository for PSS R package
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PYRAXML2 – a python wrapper for RAxML-VI-HPC
This is a python script that reads nexus data files and prepares the necessary input files and commandline options for RAxML.
BETA VERSION – UNDER DEVELOPMENT
Note: Biopython (www.biopython.org) is needed to run pyraxml2.
Download pyraxml2
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TEST FOR TREE COMPATIBILITY: COMPAT.PY
Kauff, F., Lutzoni, F. 2002. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol. Phyl. Evol. 25: 138-156
Note: Biopython (www.biopython.org) is needed to run compat.py.
Download Python program (all platforms, zip archive)
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AMBIGUOUS REGIONS CODING: ARC
Miadlikowska, Lutzoni, Goward, Zoller, Posada (2003) “New approach to an old problem: Gap-rich regions from ITS and rDNA large-subunit are incorporated into phylogenetic analyses to resolve the Peltigera canina species complex.”, Mycologia 95(6):1181-1203.
Download Python program (all platforms, zip archive)
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RANDOM TREE SAMPLING: RT
Samples trees randomly or stepwise from a given input file. A “burnin” can be specified to skip initial trees.
Download Python program (all platforms, zip archive)
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COMPARATIVE PHYLOGENETIC METHODS
Pagel, M. and Lutzoni, F. 2001. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. In Biological Evolution and Statistical Physics. M. Laessig (Ed.), Springer Verlag (submitted January 18, 2001).
Lutzoni, F., Pagel, M., Reeb, V. 2001. Major fungal lineages are derived from lichen symbiotic ancestors.Nature 411:937-940.
Download publication (PDF file)
Lutzoni, F., and Pagel, M. 1997. Accelerated evolution as a consequence of transitions to mutualism.Proc. Natl. Acad. Sci. 94:11422-11427.
Download publication (PDF file)
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INTEGRATION OF AMBIGUOUSLY ALIGNED SEQUENCES IN PHYLOGENETIC ANALYSES: INAASE
Lutzoni, F., Wagner, P., Reeb V., and Zoller, S. 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49:628-651.
Here you will find the most recent version of INAASE. It has been tested on Mac OSX, Windows XP and Linux (Debian 4.0, desktop version, but any other distro should also work). It works only with Java 1.5 or higher installed. In this version, the alignment algorithm has been improved.
Download INAASE 3.0 (ZIP file)
Previous versions of INAASE:
Download INAASE for PC (ZIP file)
Download INAASE 2.3b for MAC (Stuffit file)
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PARTITION HOMOGENEITY TESTING
Barker, F. K., and Lutzoni, F. 2002. The utility of the incongruence length difference test. Systematic Biology 51:625-637.
Lutzoni, F., and Barker, F. K. 1999. Sampling confidence envelopes of phylogenetic trees for combinability testing: A reply to Rodrigo. Systematic Biology 48: 596-603.
Lutzoni, F. 1997. Phylogeny of lichen- and non lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets. Systematic Biology 46:373-406 (journal cover).Download data set (Stuffit file)
TreeBase web site
Lutzoni, F., and Vilgalys, R. 1995a. Integration of morphological and molecular datasets in estimating fungal phylogenies. Canadian Journal of Botany 73(Suppl. 1): S649-S659. Downloadable data sets:
TreeBase web site
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A NEW TEST FOR MONOPHYLY IS DESCRIBED IN THIS PAPER
O’Donnell, K., Lutzoni, F., Ward, T., and Benny G. 2001. Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia 93:286-296.
Download publication (PDF file)
Download data set (Stuffit file)
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A NEW METHOD TO CONVERT CONTINUOUS CHARACTERS INTO DISCRETE CHARACTERS IS DESCRIBED IN THIS PAPER
Lutzoni, F., and Brodo, I. M. 1995. A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized Ascomycotina). Systematic Botany 20: 224-258.
Download publication (PDF file)
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A METHOD IS DESCRIBED TO OBTAIN STEP-MATRICES WITH UNEQUALY WEIGHTED COSTS (program STMatrix written by Stefan Zoller)
Miadlikowska, J., McCune, B. and Lutzoni, F. 2002. Pseudocyphellaria perpetua, a new lichen from Western North America. The Bryologist 105:1-10.
Here you will find the most recent version of STMatrix. It has been tested on Mac OSX, Windows XP and Linux (Debian 4.0, desktop version, but any other distro should also work). It works only with Java 1.5 or higher installed.
Download Java STMatrix 3.0 (Zip file)
Previous version of STMatrix:
Download PPC STMatrix 2.2 (Stuffit file)