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christianparobek / skeleSim

Null models, performance testing, and power estimation with population simulations
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Multiple chromosomes? Multiple marker types? #23

Closed EricArcher closed 8 years ago

EricArcher commented 8 years ago

I'm reformatting how loci are specified for fastsimcoal, and I want to clarify/remember a few things:

1) Are we allowing simulation of more than one chromosome? If so, how are we specifying recombination?

2) I believe we decided on allowing simulation of only one marker type (sequence, SNP, microsats) at a time, right? If so, I assume that we are allowing loci on the same chromosome with different parameters (e.g., multiple sets of microsatellite loci with different mutation rates)...

smhoban commented 8 years ago

I think its ok for now to assume either fully linked or fully independent loci. Specifying recombination could be tricky. But that is my first thought?

Yes I think we should allow different mutation rates. It could be input in the way that Allan allows allele frequencies to be input, which is nicely dynamic

On Sun, Feb 21, 2016 at 11:41 PM, Eric Archer notifications@github.com wrote:

I'm reformatting how loci are specified for fastsimcoal, and I want to clarify/remember a few things:

1) Are we allowing simulation of more than one chromosome? If so, how are we specifying recombination?

2) I believe we decided on allowing simulation of only one marker type (sequence, SNP, microsats) at a time, right? If so, I assume that we are allowing loci on the same chromosome with different parameters (e.g., multiple sets of microsatellite loci with different mutation rates)...

— Reply to this email directly or view it on GitHub https://github.com/christianparobek/skeleSim/issues/23.

Sean Hoban Tree Conservation Biologist The Morton Arboretum http://www.mortonarb.org/ 4100 Illinois Rt 53, 3rd Floor Research Bldg, room 324, Lisle, IL 630-719-2419

New publications!! Accounting for the nested nature of genetic variation http://onlinelibrary.wiley.com/doi/10.1111/oik.02760/abstract Oikos 2016 Exploring seaweed population dynamics http://onlinelibrary.wiley.com/doi/10.1111/jpy.12366/abstract Journal of Phycology 2016 Loci under selection in expanding tree populations http://onlinelibrary.wiley.com/doi/10.1111/mec.13234/abstract Molecular Ecology 2015 Designing optimal seed collection protocols http://www.sciencedirect.com/science/article/pii/S0006320715001767 Biological Conservation 2015 Using ABC to understand invasive species establishment http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201538a.html Heredity 2015

research webpage: http://sites.google.com/site/hoban3/ ResearchGate Profile: http://www.researchgate.net/profile/Sean_Hoban/ food blog: http://cuisineraveclevin.blogspot.it/ blog about invasive species: http://invasivore.org/

EricArcher commented 8 years ago

Sounds good. I've now set the fastsimcoal code so that only one type of marker (dna, msat, or snp) can be simulated, but multiple loci (stretches of sequence, msat, or snp loci) can be simulated on a single chromosome as well as across multiple chromosomes.