From time to time, people have asked me to supply
various programmes used in our research or teaching. (More recently I've
here added particularly useful but not well known packages from other labs, but
whose location I might otherwise forget). The downloadable, self-unpacking programmes
below come with notes on how to use them. Apart from (5), they are all DOS-based,
but should run in MS-DOS or "Command Prompt" windows on anything up
to and including Windows XP. If you are not familiar with DOS commands,
you should get help, because the programs will often perform oddly if run in a
DOS window from within Windows. It is almost always best to run DOS or command
prompt programmes in "full screen" mode.
These programs are supplied as self-unpacking ZIP files. They should be downloaded into their own folder, and then unpacked by running the *.EXE self-unpacking file.
1) Randomization test for genetic diversity differences
between pairs of populations using allozymes and/or mtDNA.
PERMUTE.EXE (32-bit DOS), written by Martin Brookes, and modified by J. Mallet. See also: Brookes, M.I., Graneau, Y.A., King, P., Mallet, J.L.B., Rose, O.C. & Thomas, C.D. (1997). The genetic consequences of artificial introductions and natural colonizations in the British butterfly Plebejus argus. Conservation Biology 11: 648-661.
2) Beta-binomial test for hierarchical analyses
of count data, for example testing brood survival data in crosses between taxa.
BETABINO.EXE (32-bit Windows Console), written by Ziheng Yang (note, will run on 32-bit systems, Windows 95+ only). See also: Jiggins, C.D., Linares, M., Naisbit, R.E., Salazar, C., Yang, Z. & Mallet, J. (2001). Sex-linked hybrid sterility in a butterfly. Evolution 55: 1631-1638. REPRINT .
3) Programs to demonstrate natural selection and
NATSEL.EXE and DRIFT.EXE (16-bit DOS), written by Jim Mallet.
4) Program to calculate linkage disequilibria
for loci of arbitrary dominance.
DIS.EXE (16-bit DOS), written by Jim Mallet. Dominant, recessive, and codominant loci are allowed (e.g. in colour-pattern loci, AFLP loci, RAPDs etc.). Cytonuclear disequilibria can also be estimated (e.g. mtDNA haplotype vs. allozyme loci). For dominant genes, estimates assume Hardy-Weinberg at each locus. Only two alleles per locus are allowed, so this program is mainly useful for hybrid zone studies or studies of natural hybridization. It would be useful for SNPs but not for microsatellites which have many more than two alleles. The program uses a likelihood-based method equivalent to that in Hill WG (1974) Heredity 33: 229-239. See also: Dasmahapatra, K.K., Blum, M.J., Aiello, A., Hackwell, S., Davies, N., Bermingham, E.P. & Mallet, J. (2002). Inferences from a rapidly moving hybrid zone. Evolution 56: 741-753. REPRINT
5) Program to randomize mimicry associations
RANDMIM.EXE (32-bit WINDOWS). Specially written for Keith Willmott, and extremely specialized; not likely to be useful for anyone else! More details on the "Explanations" worksheet of HOSTMIM.XLS supplied in the package. See: Willmott, K.R. & Mallet, J. (2004). Correlations between adult mimicry and larval hostplants in ithomiine butterflies. Proceedings of the Royal Society of London, Series B 271 (Biology Letters S5): S266-S269. REPRINT
6) Program to test for recombination in a DNA sequence or haplotype, by testing for evidence for a correlation between linkage disequilibrium and distance along a sequence. RecombiTEST by Gwenael Piganeau (online test). Tests are separately done with two standardized measures of disequilibrium (R2, and with D/Dmax , or D', and measure the decline in correlation of the disequilibrium measure with distance along a sequence in a sample of aligned haplotypes. The correlation coefficient is bootstrapped 1000 times to test for significance. Programme automatically deletes from the alignment gaps and sites with more than two bases (This is not from our lab, but I couldn't find the website via an internet search, so I have put the link online partly for our own convenience. As used in: Piganeau, G., & Eyre-Walker. A. 2004. A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity 92:282-288.)
7) G-Test G.EXE. Simple calculator for G and chi-square (X-square) values and degrees of freedom for n x n homogeneity test tables (16-bit DOS).
8) Cline-fitting, C6, C7 etc. for fitting phenotypes or allelic data, including the the possibility of fitting bimodal hybrid zones for the first time that I know about. Thomas LeNormand.