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Description:
popABC is an Approximate Bayesian Computation method to estimate demographic historic parameters (e.g. population size, migration rate, splitting events) within a Isolation with migration population model.
This software is freeware and the source code is available upon request.
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INTFILE
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Hi,
i am running popabc in a cluster and getting the message "error::
INTFILE couldn't be created" after the simulation step. I guess this
is beacuse I have no permission to delete or overwrite files in the
folder. Any suggestion to bypass it?
many thanks in advance
ferran
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mutation rate
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Dear Joao,
I am a little bit confussed on the units for the mutations rate. For a
set of independent SNPs (humans), should it be set to the human mut
rate 10 -8?
many thanks
ferran
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opening len files in popabc
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Hi,
I have been trying to run PopABC using my own len files generated
using the convert genepop file to table file options on the tools menu
in popabc.exe, but the program would not recognise the files. I also
tried running the program using the example toytable.len file and once
again it could not recognise the file. Am I missing something... more »
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recombination rate?
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Hi Joao,
The popABC manual says "The simulation method models each locus as
having segregated independently over time" because the IM model
assumes free recombination between loci.
Yet, the program takes priors on recombination rates.
This seems to contradict the assumption.
Thanks for your help.... more »
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Nm=H???
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Hi Joao,
In the target files and the simulated data files (.dat), the value of
Heterozygosity (H) always equals that of Nm (for a given population).
Unless I'm mistaken, this shouldn't be.
Here an example of simulated data (2 populations, microsat marker):
[top|marker|avMutM|sdMutM|avRe cM|sdRecM|t1|Ne1|Ne2|NeA1|mig1 |mig2]... more »
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Posterior=prior
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Hi,
I've tried PopABC to estimate migration rates between 3 pops (using
microsat data). I've set fairly wide priors for all parameters (not
knowing much a priori), except the mutation rate so that the simulated
data had realistic levels of heterozygosity. My intention was to
adjust the priors after test runs.... more »
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OS X: the PowerPC architecture is no longer supported
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Dear Joao,
Trying to run the program on my intel-based Mac, I got the error
message that the PowerPC architecture was no longer supported. Indeed,
the current version of Mac OS X doesn't support PowerPC binaries, only
x86 or IA64 binaries.
Is there a way to get the program running on my Mac under OS X? I... more »
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Microsat allele lengths?
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Hi everyone,
Some summary statistics computed by PopABC use the length of microsat
alleles (varL,kurL). But nowhere in the data file specification (.len)
do I see any mention of allele lengths.
How do I encode allele lengths in my genetic data?
Thanks for your help.
Jean
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Modelling admixture
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Dear Joao, I was wondering if there is anyway of modelling admixture in PopABC? Look forward to hearing from you Regards, Vishnupriya
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modelling a genetic barrier
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Dear popABC developers, I would also like to congratulate you on creating this really useful software! My question is the following: I want to model the genetic barrier among, say, 4 populations with the following topology (in order to visualise the topology properly, please change to courier font):... more »
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