Michael Krawczak, Kiel 07.01.2002
Dear Colleagues,
Below please find a compilation of computer programs, written by myself, which I am happy to share with the scientific community. Anybody who wishes to make use of them for non-commercial purposes is invited to download the programs, and to work with them free of charge. However, those with commercial interests in their usage are kindly requested to contact me first.
Please remember that the programs were written for scientific purposes, some of them quite a long while ago, and have never been designed to look sexy. Nevertheless, useful suggestions, comments, criticisms serving to improve the programs are highly welcome.
With all best wishes
MK
The programs:
ASP is a power calculator for gene mapping using a sibpair design (concordant or discordant). ASP employs a diallelic model for the trait locus and simulates parental and offspring genotypes under Hardy-Weinberg equilibrium. Marker locus genotypes are simulated conditional upon the inheritance pattern at the trait locus and tested for non-Mendelian ibd sharing. For discordant sibs, an unrestricted likelihood ratio test is used; for affected sibpairs, the power of the dataset is also determined using a restricted likelihood ratio test. The program ASPSHARE complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. It should therefore be used prior to any time-consuming simulations to assess whether a model is sensibel.
Download the ASP or ASPHARE program or ASP documentation or WinASP program.
EASYPAT is a computer program that allows calculation of likelihood ratios for single locus data, comparing specific types of simple hypotheses regarding the familial relationships involved. Currently, these hypotheses include (i) parenthood vs. non-parenthood in duos comprising parent and child, (ii) paternity vs. non-paternity in trios comprising mother, child and alleged father, and (iii) full sibs vs. halfsibs in trios comprising one parent and two children.
Download EASYPAT program or the EASYPAT documentation.
Two programs, MUTPROF and MUTCOMP, are available for the comparison of mutation profiles. MUTPROF is a Monte-Carlo-Markov-Chain implementation of the hypergeometric test for sparse 3-dimensional contingency tables (in the spirit of Fisher's exact test). It allows the comparison of up to 200 positions within the same gene, but between different tissues and/or species. MUTCOMP serves to compare two nucleotide substitution matrices for one or more, possibly different genes, tissues or species, taking the expected mutation frequencies into account. Testing is via bootstrapping.
Download MUTPROF program, the MUTCOMP program or the MUTATION documentation.
The program FINDSIRE has emerged from the large scale paternity testing project performed on the rhesus macaques of Cayo Santiago (Nuernberg et al. 1998, Am J Primatol 44, 1-18). The software allows to identify mothers or sires by means of the comparison of a large number of potential parents, typed at single locus DNA markers, with given infants or parent-infant duos. Potential parents with more than a certain number of mismatches in their DNA profiles are excluded from parenthood whilst those not excluded are reported for further analysis.
Download the FINDSIRE program or the FINDSIRE documentation.
PATERN is a computer program for the calculation of paternity probabilities from the multilocus DNA profiles of trios, comprising mother, child and putative father. The mathematical model employed is that published in (Krawczak & Bockel 1992, Electrophoresis 13, 10-17).
Download the PATERN program or the PATERN documentation.
The program FINGCOMP allows calculation of the joint likelihood of multilocus DNA fingerprints observed in pedigrees of arbitrary structure.
Download the FINGCOMP program or the FINGCOMP documentation.
The program HAPMAX allows to calculate maximum likelihood estimates of haplotype frequencies. Originally, the program was designed for the analysis of markers associated with recessive disorders (such as CF), and the layout still reflects this initial purpose. However, HAPMAX can be applied to a much broader range of problems, including TDT-like comparisons of transmitted and non-transmitted haplotypes in trios comprising affected individuals and their parents.
Download the HAPMAX program or the HAPMAX documentation.
The program MUTPRED generates mutability profiles of amino acid sequences from the corresponding cDNA sequence. The procedure is described in detail in (Cooper & Krawczak 1990, Hum Genet 85, 55-74). The program generates UNWEIGHED profiles as described, and WEIGHED profiles for which the relative mutabilities are multiplied by the likelihood of clinical detection depending upon chemical difference.
Download the MUTPRED program or the MUTPRED documentation. Note that you run the program you also need the MUTPRED message file as well.
The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences Hum Genet (1992) 90: 41-54 (PDF 12MB)
Contact address:
Prof. Dr. Michael Krawczak
Institut für Medizinische Informatik und Statistik
Brunswiker Str. 10
D-24105 Kiel
Germany
Tel.: +49 431 597 3200
Fax.: +49 431 597 3193
Email: krawczak@medinfo.uni-kiel.de