Download MalHaploFreq user manual

Contents:
1. Basic principles: using Maximum Likelihood (ML) methodology to
estimate allele and haplotype frequencies from blood samples (page 3).
2. Decisions required before data analysis (page 7).
3. Running the analysis (page 10).
4. Checking the analysis: checks you should make (page 16).
5. Checking the analysis: checks I have made (page 18).
6. How to tell if frequencies differ between datasets (page 19).
7. Acknowledgements (page 21).
Appendix 1: The MalHaploFreq algorithm (page 22).
Appendix 2. Alternative algorithm (page 26).
Appendix 3. The original version of the Smith and Penny algorithm (page
29).
Appendix 4. Simple tests to check programme is working (page 31).
Appendix 5. History of programme versions and updates (page 32)
References (page 33).
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