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Teaching in the Collaborative Learning Centre |
ReticulateHere is the code for reticulate, to accompany this paper:Jakobsen, I.B. & Easteal, S. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences CABIOS (now "Bioinformatics") 12: 291-295 (1996) The program is written in C, and requires a *nix-type system with X11 (most *nix these days) A text file with instructions, both for compiling and running the program reticulate.c The main program XPlot.c, required to display graphics on screen XPlot.h, required to display graphics on screen makefile gamblobin.gde, the globin data set from the paper, so you can reproduce Fig.2
PartimatrixHere is the code for partimatrix, to accompany this paper:Jakobsen, I.B., Wilson, S.R & Easteal, S. The partition matrix: Exploring variable phylogenetic signals along nucleotide sequence alignments Mol. Biol. Evol. 14: 474-484 (1997) The program is very similar to reticulate. Note that they use similar, but different XPlot.h and makefiles, so it's worth downloading them into separate directories/folders. A text file with instructions, both for compiling and running the program partimatrix.c The main program pmXPlot.c, required to display graphics on screen XPlot.h, required to display graphics on screen makefile pseudaut.gde, the pseudoautosomal boundary data set from the paper, so you can reproduce Fig.2. (Fig.4 uses "reticulate", above)
This software is provided for free, as is, with no warranty express or implied, etc, etc.
Contact details:email i.jakobsen@uq.edu.auphone +61 7 3365 7037 fax +61 7 3365 6136 Department of Mathematics University of Queensland Brisbane QLD 4072 Australia |