MIGRATE 4.2 Files in this directory should not yet used for publications, but for feedback. If you try the program let me know about whether your results match your expectation, whether you encounter crashes (report all details: hardware, OS, log, outfile fragment, parmfile, infile) Migrate-4.2 should be able to take your old parmfile and infile and run it, it will issue some warnings because the start parameter setting changed, simply resave in the new version. If you want to know what changed, you can do cp parmfile parmfile.old migrate-n parmfile [save the parmfile] on mac: opendiff parmfile parmfile.old on linux: diff parmfile parmfile.old on windows: ?????? The manual is not up to date yet, and will take a moment, I am working on the paper to describe population splitting mechanism, which has priority. What I want you to do: - run your data for migration and population size estimation or compare models - the menu has changed some, experiment with that More to come, this README will now change regularly and is the spot to go to learn about: - divergence - assignment - haplotyping March 2015 Peter Beerli beerli at fsu dot edu Divergence: # # Custom migration model # # Syntax: custom-migration={ab..bbab..ba ... a} # the {} is a square matrix with values for the population sizes # on the diagonal and migration rates or divergences off-diagonal # the values _a_ for the diagonal can be any of these: # c constant, define the values in the theta option # * free to vary, the default is * for every parameter # m mean of theta, this can be a subgroup # for example: theta 1-3 are averaged, thetas 4,5 are estimated # # the values _b_ for the migration rates can be any of these: # c constant, the value needs to be defined in the migration option # * migration rate free to vary, this is the default # d row population is offspring of column population # D row population is offspring of column population with migration # # m mean of M_ij, this can be a subgroup of migration rates # for example the M_1-3i are averaged and M_4,5i are estimated # M means of 4Nm (diploid), 2Nm (haploid), Nm (mtDNA, Y-chromosome) # s symmetric migration rates M # S symmetric migrants 4Nm # an example for 5 populations could look like this: # custom-migration={*s00s # s*s00 # 0s*s0 # 00s*s # s00s*} # this describes a circular stepping stone model with 5 symmetric rates # and independent sizes, a very basic stepping stone with 2 parameters would # look like this custom-migration={mm00m mmm00 0mmm0 00mmm m00mm} # # population splitting example with 3 populations: # custom-migration={*D0 **d 00*} # *-----1 1 receives migrants from 2 # |MMMMM and split from 2 # *--------2 2 receives migrants from 1 # | and split from 3 # ---------*--------3 3 is the persisting ancestor custom-migration={**} # Assignment for best operation use 0, 1, 2, .... as the first letter in the individuals and the numbers are population assignments, individuals that need to be assigned to a population will get a ?. for example this 2 3 testdata (s3 s4) (s5) 3 location Arbon 0ind1 ACATGGANCGGA 0ind2 ACATGGANCGGA 0ind3 ACATGGANCGGA 3 location Romanshorn 1ind4 ACATGGANCGGA ?ind5 ACATGGANCGGA ?ind6 ACATGGANCGGA ind5 and ind6 needs assignment to a population (they could be added to population 1 instead of 2. In the parmfile you will need to option: # assign= YES will assign individuals to populations # with '?' as first character assign=YES You can change that also using the menu in DATA use menu 15 15 Assign individuals [?name in data] to population