the migration model, is there anything else that needs to be changed to evaluate the divergence of one population from another (with or without gene flow)? I'm attaching a parmfile

most complicated model is >>> Tamura-Nei + Gamma >>> >>> peter >>> >>> >>> >>>> On Apr 4, 2023, at 6:05 PM

that the mutation rate is not really known and estimated, but looking at the different loci there is variation that has at least two sources: 1. MCMC error, 2. different mutation rates

the Brownian model because it is fast and delivers similar result as the explicit stepwise model. the stepwise model is horribly slow in comparison; upon a quick test, I seem to have

the option mutation=ESTIMATE this option will not work with your type of data, you need dated samples at different time points set it to mutation=CONSTANT Estimating a mutation rate

run another mutation model than jukes cantor and/or look into unidirectional migration. Peter > On Feb 18, 2021, at 13:45, Christine Ewers wrote: > > Dear Peter, > That

the migration model.] The easiest to construct complex migration models is to use the a texteditor and edit the parmfile, search for the option custom-migration, Peter > On May

-island model > > A question though. I reduced the migration limit because most of the parameters are peaking around zero (this was suggested in some tutorial). Here you can see

Markus, the config.log looks fine to me Ignore the warning messages in the mpis_log.txt, they only address missing return values for the scanf and

the brownian model, I would > expect that you see fewer mutations with that which will lead to lower > population sizes, I then would use that as a caveat in discussing the > results

running the model 3 times >> now but it still gives me the same error messages. >> >> I am working with data of a bit over 1000 SNPs (and 4 to 5 populations >> with

Hello Migrate support group, I am currently trying to infer the direction of gene flow in four populations and using migrate-n to do so. I am using

Finally I post the answers back to the net> how to convert a run that was done using Theta and M to Theta and xNm if the bayesallfile is available.

simpler mig model. You could even start simply by setting only one population. If you really want to have more than one pop, would you have a sensible way to divide these populations in

by a mutation rate of 0.005 (as for microsatellites), to obtain a comparable value of *m* estimated from Bayesass. My results from Migrate are: M2 -> 1 = 13.833 (immigration from

. Change mutation model > 5. One category site > 6. One region of substitutions rates. > > I am thinking that I am on the right place to change so I should choose option 6 and

with unknown mutation model # STEPWISE MUTATION: usable for microsatellite data or # other markers with stepwise change # from one allele to another # [singlestep versus multistep

What about mutation models? What to do with sequences which are under variying selection pressures depending on the sites? > > Dated samples will need an additional file, I suggest

eg the mutation model may be important here) thus there could be support for a particular direction. Although I would expect considerable uncertainty about that direction when enough

as the mutation model (but you will > need to get the alpha parameter of the Gamma distribution from somewhere > else). > It seems that your 9 parameter model is on the upper limit

5 population model (I suggest to use a model that allows fewer than 20 migration rates) and the model with 4 populations (the two populations combined), I assume these model may have

I'm trying to run a fairly small msat dataset (3 pops, 209 individuals, 5 loci) on a 1600 MHz,

Hi I have a migrate run of one mtDNA sequence, 7 populations, full migration model and the pdf

notes explaning mutation models (http://people.sc.fsu.edu/~pbeerli/BSC-5936/09-19-05/mutation-model-III.pdf), but some figures are missing in this PDF file. It would be

the brownian mutation model - perhaps test migrate on a small dataset (2 population) to find out how long it runs? - skim the migrate-support list Peter On Dec 4, 2012, at 1:25 AM, Vishal

On Nov 30, 2012, at 9:45 AM, bibek yumnam <bibek.yumnam@gmail.com> wrote: Hi Peter, I am

: - mutation=DATA - harmonising sample sizes by randomly excluding individuals from the two larger pops until all pops were of same samples size - I found one additional problem: I realised

using SMM model. Thank you for troubleshooting this and my apologies for incorrectly shifting the blame on migrate-n :). Vikram On Sat, May 12, 2012 at 10:56 AM, Peter Beerli wrote:

of the mutation model therefore >> you will need to live with the rounding up or down [I may include the correct fractional repeat number into the brownian motion model as that

brownian motion mutation model. > - Heterozygosity excess signatures decays very quickly, I guess if you would know the population sizes than one could see this over a longer time