A survey of current software for linkage analysis.

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• A wide array of software tools is available for genetic linkage analysis.
• Evaluating and comparing these software packages is crucial for researchers.
• Understanding the strengths and limitations of each tool aids in selecting appropriate methods.

Purpose of the Study:

• To review and compare prominent software packages used in genetic linkage analysis.
• To highlight the performance and specific applications of different analytical tools.
• To identify areas for future development in genetic analysis software.

Main Methods:

• Review of widely recognized genetic linkage analysis software.
• Categorization of software based on analytical approaches (parametric, non-parametric, variance components).
• Assessment of computational performance and range of analyses offered by each package.

Main Results:

• GENEHUNTER provides extensive analyses but is outperformed by specialized programs for specific tasks.
• FASTLINK and VITESSE excel in parametric analysis.
• ALLEGRO and MERLIN are optimized for non-parametric analysis.
• SOLAR is recommended for variance components analysis.
• SIMWALK2 and SUPERLINK show potential for improving computational limits.

Conclusions:

• Specialized software often offers better performance than comprehensive packages for specific genetic linkage analysis tasks.
• Future software development should focus on enhanced user interfaces and standardized data formats.
• The choice of software depends on the specific analytical needs of the genetic study.