I tried estimating effective population size and migration rate using Migrate-n based on both Bayesian and Maximum likelihood approaches. However, this software is not turning out useful for my data. I do not know if my data needs lot of work to estimate these parameters using migrate-n. My data is based on microsatellite genotypes of diploid species. Can anyone suggests other software that might help me? Also if you have input file sample, it will be great since I have less time.
Hi,
Your question is very interesting one. Software and to estimating effective population size and migration rate.
For software:
http://cteg.berkeley.edu/~nielsen/resources/software/
For references:
http://www.genetics.org/content/163/1/429.long
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2656.2007.01249.x/pdf
Dear Niraj,
You can also use MLNE. This is a program used for calculating maximum likelihood estimates of effective population size (Ne) and migration rate from the observed temporal and spatial differences in marker allele frequencies.
You can dowload the software from the following site:
https://www.zsl.org/science/software/mlne
Good luck!
Dear Niraj,
If you don't have temporal data you can also try NeEstimator v2 for estimating effective population size:
http://www.molecularfisherieslaboratory.com.au/neestimator-software/
And BayesAss for estimating migration rate, though you have to be careful that you comply with the assumptions and check for convergence properly:
http://www.rannala.org/?page_id=245
Meirmans 2014, Mol Ecol Res. doi: 10.1111/1755-0998.12216
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