Bioinformatics Advance Access originally published online on September 3, 2004
Bioinformatics 2005 21(3):405-407; doi:10.1093/bioinformatics/bti009
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses
1 Division of Nephrology, Department of Medicine, Medical University Clinic at the University of Würzburg Würzburg, Germany
2 Department of Clinical Biochemistry and Pathobiochemistry, Medical University Clinic at the University of Würzburg Würzburg, Germany
3 Institute of Medical Genetics, Charité, Humboldt University Berlin Augustenburger Platz 1, 13353 Berlin, Germany
*To whom correspondence should be addressed.
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Abstract |
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Summary: We have generated the program easyLINKAGE that combines automated setup and performance of linkage analyses and simulation under an easy to handle graphical user interface for Microsoft Windows 2000/XP and standard UNIX systems. The program package supports two-point linkage analyses (FastLink v4.1 and SPLink v1.09), multi-point linkage analyses [GENEHUNTER v2.1, GENEHUNTER-PLUS with the emendation by Kong and Cox v1.2 (allele sharing modelling)] and the simulation package SLINK v2.65, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P-values and other parameters.
Availability: http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm
Contact: tom.lindner{at}mail.uni-wuerzburg.de
Supplementary information: Supplementary information is available on the website.
Most of linkage analyses software was traditionally developed for UNIX environments. Availability and professional use of UNIX restricted calculations to a limited number of experienced users. Nowadays researchers want to analyze their genotypes immediately. However, this requires the upload of genotyping files from DOS- or Macintosh-based computer systems onto UNIX clusters, the knowledge of UNIX commands and the generation of the appropriate setup files for running linkage programs.
We think there is a need for programs that enable fast and automated linkage analyses in the same environment under which the genotypes were generated. Since most PCs run Microsoft Windows this operating system is our priority. Furthermore, a better input and output of data in a graphical format, and the automatic assembly of genotypes with the pedigree file would save much time.
We have generated a PERL/Tk-based software for Microsoft Windows 2000/XP that fulfills this task for linkage programs, such as GENEHUNTER (Kruglyak et al., 1996), GENEHUNTER-PLUS with ASM (Kong and Cox, 1997), FastLink (Cottingham et al., 1993), SPLink (Holmans, 1993; Holmans and Clayton, 1995) and SLink (Ott, 1989). Detailed installation and running instructions, the structure of the input files and the software easyLINKAGE are available on our website.
Figure 1a shows the appearance of the main screen. The use is intuitive and self-explaining. The user can choose among analyses on all chromosomes, single chromosomes and sets of chromosomes. Allele recoding as well as breaking marriage loops by the ‘unknown –l’ option in the FastLink part of the program (Becker et al., 1998) will be automatically carried out using easyLINKAGE. It enables the definition of individual options for the provided linkage analysis programs. Furthermore, easyLINKAGE provides the use of different allele frequency algorithms. This is an extension of the original programs and allows a more versatile use. However, every algorithm has its specific advantages and pitfalls. The user can choose among ‘codominant’, ‘All individuals from ABI file’, ‘All individuals from pedigree file’, ‘First person of an ASP’ and ‘Founders only’.
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LCP, QUIKLINK and GLUE are other attempts to streamline classical linkage programs. easyLINKAGE provides almost all options of these programs plus other features. The available options and the description of the allele frequency algorithms can be found in the manual on our website. Although LCP and QUIKLINK support exclusively the classical LINKAGE package with its extension and modifications (FastLink, Vitesse, etc.), easyLINKAGE enables the additional use of GENEHUNTER/-PLUS, SPLink and SLink. Packages currently supported by GLUE are FastLink, GENEHUNTER, MERLIN, Unphased and Transmit.
The handling of FastLink (or LINKAGE) allows a fair comparison of all programs. LCP, QUIKLINK and GLUE require pedigree files that contain the pedigree information and the appropriate genotypes for every marker. QUIKLINK in particular utilizes only post-MAKEPED files. The user must generate these files in additional steps. easyLINKAGE does the assembly of the genotypes with the pedigree file automatically and the genotyping files from any sequencing system can be used right away. Therefore, easyLINKAGE needs just one pedigree file and the genotyping files instead of pedigree files with genotypes for every single marker. In contrast to LCP, QUIKLINK and GLUE, a datafile containing the inheritance model parameters must not be generated manually since easyLINKAGE provides an interactive input of the most commonly used parameters and options. In this regard, we decided to use a fixed set of recombination fraction values (0.000, 0.001, 0.010, 0.050, 0.100, 0.150, 0.200, 0.300, 0.400 and 0.500), where GLUE for instance is more versatile. In our experience, this strategy represents a good compromise between saving computing time and the extraction of more genetic information. Therefore, only MLINK but not ILINK is supported.
Further, some FastLink programs cannot deal with the marker file or pedigree structure file names longer than the DOS 8.3 limit letter convention. easyLINKAGE contains an algorithm that enables the usage of long file names. Also, families and subject IDs in the pedigree file will always be temporarily renumbered during the run in order to guarantee an error-free processing of all linkage programs. GENEHUNTER and FastLink for instance have trouble with long identifiers.
Another benefit is the use of marker maps in easyLINKAGE. MARSHFIELD, DECODE and LDB maps with marker, genetic positions for sex-averaged, female and male situations are provided. easyLINKAGE decides during the run whether a marker is on the X or another chromosome and chooses the correct program routines automatically. It also enables an automated analysis of individual chromosomes with correct marker distances and without additional editing work by the user.
In addition, the user can analyze models under the assumption of different allele frequency algorithms and apply them to different pedigree structure files. easyLINKAGE provides graphical outputs in postscript format for many different parameters (Fig. 1b). Postscript files can be easily converted into PDF files using the Acrobat Distiller software. Neither LCP nor QUIKLINK contain these features. GLUE does many similar analyses when compared with our program. It is a web-interface rather than a stand-alone program enabling the work under different operating systems. This might be beneficial in certain situations.
In our laboratory, we were able to automate all procedures that were usually required for generating input files and running the analyses. We have extended the linkage programs by introducing a graphical output to the most important parameters. The easyLINKAGE package allows generating and analyzing genotypes within the same operating systems without the need of adapting files for the use in other operating systems. The software is free of charge; the extension of the source code is appreciated. We have used a modular programming structure so that other linkage programs can be implemented if needed.
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Acknowledgments |
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We thank Drs Alejandro Schaffer, Jurg Ott, Michael L. Frigge, Leonid Kruglyak and David Clayton for the permission to recompile the source code of their program for the use in Microsoft Windows and for publishing the binaries on our website. T.H.L. was supported by grants from the Deutsche Forschungsgemeinschaft (DFG; LiDFG768/3-1/3-3, LiDFG768/4-1/4-2). K.H. was supported by a grant from the Deutsche Forschungsgemeinschaft (SFB 577, project A9).
Received on July 14, 2004; revised on August 30, 2004; accepted on August 31, 2004
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REFERENCES |
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TOPAbstractREFERENCES |
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Becker, A., Geiger, D., Schaffer, A.A. (1998) Automatic selection of loop breakers for genetic linkage analysis. Hum. Hered., 48, 49–60[CrossRef][Web of Science][Medline].
Cottingham, R.W., Jr, Idury, R.M., Schaffer, A.A. (1993) Faster sequential genetic linkage computations. Am. J. Hum. Genet., 53, 252–263[Web of Science][Medline].
Holmans, P. (1993) Asymptotic properties of affected-sib-pair linkage analysis. Am. J. Hum. Genet., 52, 362–374[Web of Science][Medline].
Holmans, P. and Clayton, D. (1995) Efficiency of typing unaffected relatives in an affected-sib-pair linkage study with single-locus and multiple tightly linked markers. Am. J. Hum. Genet., 57, 1221–1232[Web of Science][Medline].
Kong, A. and Cox, N.J. (1997) Allele-sharing models: LOD scores and accurate linkage tests. Am. J. Hum. Genet., 61, 1179–1188[CrossRef][Web of Science][Medline].
Kruglyak, L., Daly, M.J., Reeve-Daly, M.P., Lander, E.S. (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am. J. Hum. Genet., 58, 1347–1363[Web of Science][Medline].
Ott, J. (1989) Computer-simulation methods in human linkage analysis. Proc. Natl Acad. Sci. USA, 86, 4175–4178
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