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Phylogenetics - Downloadable Programs
These papers address, at least in part, fundamental issues of phylogenetic methods. Programs to implement some of the methods we have developed can be downloaded from this page.
Test for tree compatibility: COMPAT.PY
Ambiguous Regions Coding: ARC
Comparative methods
INAASE (program available)
Partition homogeneity tests
Monophyly test
Conversion of continuous characters to discrete characters
Step-matrix for molecular data (program available)
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
Downloadable Python program (all platforms, tar archive).
Downloadable Python program (all platforms, zip archive).
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.
Downloadable Python program (all platforms, tar archive).
Downloadable Python program (all platforms, zip archive).
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 (in press).
Lutzoni, F., and Pagel, M. 1997. Accelerated evolution as a consequence of transitions to mutualism. Proc. Natl. Acad. Sci. 94:11422-11427. ** This PNAS paper was the subject of an article published on the ScienceNow (AAAS) website.
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.
Downloadable PC version of INAASE(ZIP file)
Dowloadable Mac PPC version of INAASE (Stuffit file)
PARTITION HOMOGENEITY TESTING:
Barker, F. K., and Lutzoni F. 2001. Spurious rejection of phylogenetic congruence by the ILD test: A simulation study. Systematic Biology. (in review).
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). Downloadable 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 at TreeBase web site.
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. Downloadable data set (Stuffit file)
TreeBase web site
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.
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 (in review). Dowloadable PPC STMatrix program (Stuffit file) .
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Last update March 2004
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