AlphaMPSim is an important tool for designing and investigation multi parental RILs, especially MAGIC populations which require high-density genotyping.

1. I could not run ./SingleScenario.sh on my Mac. I got the following errors, where I’ve replaced part of the path by xxxxx: forrtl: severe (64): input conversion error, unit 1, file xxxxxx/AlphaMPSimRelease1/Analysis/AlphaMPSimSpec.txt forrtl: severe (64): input conversion error, unit 1, file xxxxxx/AlphaMPSimRelease1/Analysis/Scenarios/Sc1/AlphaMPSimSpec.txt (an Analysis folder was created, with subdirectories).

2. An equation showing the different terms added to simulate the phenotypes, what these terms are, what distribution they follow etc. would make it easier to understand how the phenotypes are simulated. The distinction between “true breeding value” (Page 2 line 9 column 1) and “heritability” (manual) could be explained.

3. Understanding Figure 1 would be easier if the lines separating the individuals were more visible and the 3 “phases” (parents, intercrossing, inbreeding) were indicated.

4. manual: explain how to get RunMac.sh to read files of user supplied founder haplotypes (e.g. using Sanger sequences of mouse strains, using ref sequence + VCF).

5. page 1 line 46 column 1: dot before optimization should be a comma

6. page 1 line 45 column 2: “accession” is a term used for plants mostly and might not be clear for readers who use “strains”

7. page 2 line 34 column 2: enable researchers to

8. manual page 5 ,MaxAlleleFreqForQTLForModel3And4: MAF needs to be between 0 and 0.5 rather than 0 and 1

9. manual: in four of the output files names (UnrestrictedCausitiveSitesAnimalGenotypes etc.): causative rather than causitive