for upper bounds of "q" setting

[Hj Xue]

Dear Dr Hey and group,
I met a problem of upper bounds of "q" setting in IMa2 analysis. The
distributions of "q" can not fall within
the upper bound even I set q=6000. So, how should I do?
for example, in one analysis, I used two nuclear loci, sample
size=144
Command line string : -inuclear.txt -onuclearrun4.out -j1 -hfg -hn10 -
ha0.96 -hb0.9 -m3 -t600 -q6000 -b500000 -l100000 -p357 -s763214
and, in this analysis, some of the ESS values are smalll
(log[P]=13,to=232337,tmrca0= 15,tmrca1= 31)

In another analysis (four loci, two are mitochondrial genes, two
nuclear genes), the distributions of "q" can not fall within the upper
bound either. and the ESS values are always small.
the Command line string : -ialtica3.txt -oaltica3run1.out -j1 -hfg -
hn10 -ha0.96 -hb0.9 -m100 -t1 -q400 -u0.5 -b750000 -l150000 -p357 -

Log[P] t0 tmrca0 tmrca1 tmrca2 tmrca3
ESS < 24 < 18 < 62 < 51 < 13 < 12

Looking forward to your reply!

Thanks

HJ Xue

[Miao Liu]

Can anyone introduce me some easy-use-program to estimate  δμ²       for microsatellites. This is related with the upper bound quetion.

 

Reading the IMa2 document, I learned that we can estimate the upper bound by using the geometric mean of the population mutation rate (estimators such as nucleotide diversity, Watterson's estimator, δμ²

for microsatellites. )

Many thanks,

Miao

From: Hj Xue <tir...@126.com>
To: Isolation with Migration <isolation-wi...@googlegroups.com>
Sent: Thursday, May 17, 2012 2:16:49 AM
Subject: for upper bounds of "q" setting

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[TEW]

Hi Miao Liu,

 I have the same question about setting -q,-t,-m. Have you resolved it?

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[Miao Liu]

I did not pursue that approach for setting upper bounds, instead I just ran some preliminary analyses to find out the upper bounds. In my case, -q is not a problem. It is -m that cause problem i.e. no matter how high I set -m. Sometimes the estimation of  LLR95%upper is over maximum. So eventually, I adopted Exponential setting, which seems help.

 

Hope this help. Good Luck!

Miao

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