Program documentation

Modification Environment for Genetic Analyses

• MEGA2 data conversion program documentation

Integrated programs

• SIMWALK2 documentation (Does haplotyping, location scores, and non-parametric statistics)
• Merlin
• SAGE

Linkage Analysis

• VITESSE documentation
• LINKAGE documentation (NY, USA)
• MultiMap documentation (NY, USA)
• SLINK documentation (Simulation program)
• CRI-MAP documentation (NY, USA)
• CRI-MAP documentation (BioBase, Denmark)
• CRI-MAP tutorial (BioBase, Denmark)
• SAGE SIBPAL tutorial (Ohio, USA)

Segregation and Linkage Analysis

• PAP manual

Non-parametric analysis

• APM documentation
• SimIBD documentation
• SPLINK documentation
• ASPEX documentation

Haplotyping programs

• SIMWALK2 documentation (Also does location scores and non-parametric statistics)

Quantitative Trait Analysis

• SOLAR documentation (Southwest Foundation for Biomedical Research)
• MAGE documentation
• IBD documentation
• IBDN documentation
• MIM documentation

Linkage Disequilibrium

• Disequilibrium program documentation
• HRR documentation
• TRANSMIT documentation

Utilities

• R
• The R Project for statistical computing
• The Comprehensive R Archive Network (CRAN at CMU)
• R Help Search
• Intro to R by Karl Broman
• Perl
• Intro to Perl by Karl Broman
• Awk
• GAWK Language Programming
• Unix
• Primer on basic UNIX
• An introduction to UNIX
• Others
• ANALYZE documentation
• Downfreq documentation (Allele recoding)
• Extract documentation
• MultiHomog documentation
• MultiILINK documentation
• C++ Annotations