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ChrisR
10-22-2012, 12:13 AM
Fellow Y-researchers. I like to have your review on a mutation rate model I like to use in the future for pre-surname time research: Ballantyne et al. 2010 & Burgarella et al. 2011 Simple Mean excluding 9 fast mutating markers over 0.005. For a discussion about different STR mutation rate models please see the huge MolGen The properties of Y STR's dys loci (http://eng.molgen.org/viewtopic.php?f=3&t=575) thread or open a similar thread here.

You can look at the FTDNA style table here (Papers are linked):
Ballantyne et al. 2010 & Burgarella et al. 2011 Simple Mean
http://j-l250.gen.or.at/archive/Interesting-Haplotypes-Research/MutationRates/MutRate_Ballantyne-Burgarella-Mean_FTDNA-style-Table.html

Here is the setup file for Y-Utility:
http://j-l250.gen.or.at/archive/Interesting-Haplotypes-Research/MutationRates/MutRat_Y-Utility_Setup_BallBurgMean2011-no-fast-markers-09.txt

I really appreciate if you review it (using of exact mutation rates from the papers and correct mean), especially if you are interested in testing or using it for your own research. All comments welcome.

P.S.: I know this is not perfect, but I need a handy tool for FTDNA haplotypes like Y-Utility (http://www.mymcgee.com/tools/yutility111.html) (thanks to Dean McGee) with a better mutation rate model then included.

I'm open for better (fast and easy) solutions.

MJost
11-16-2012, 04:29 PM
Fellow Y-researchers. I like to have your review on a mutation rate model I like to use in the future for pre-surname time research: Ballantyne et al. 2010 & Burgarella et al. 2011 Simple Mean excluding 9 fast mutating markers over 0.005. For a discussion about different STR mutation rate models please see the huge MolGen The properties of Y STR's dys loci (http://eng.molgen.org/viewtopic.php?f=3&t=575) thread or open a similar thread here.

You can look at the FTDNA style table here (Papers are linked):
Ballantyne et al. 2010 & Burgarella et al. 2011 Simple Mean
http://j-l250.gen.or.at/archive/Interesting-Haplotypes-Research/MutationRates/MutRate_Ballantyne-Burgarella-Mean_FTDNA-style-Table.html

Here is the setup file for Y-Utility:
http://j-l250.gen.or.at/archive/Interesting-Haplotypes-Research/MutationRates/MutRat_Y-Utility_Setup_BallBurgMean2011-no-fast-markers-09.txt

I really appreciate if you review it (using of exact mutation rates from the papers and correct mean), especially if you are interested in testing or using it for your own research. All comments welcome.

P.S.: I know this is not perfect, but I need a handy tool for FTDNA haplotypes like Y-Utility (http://www.mymcgee.com/tools/yutility111.html) (thanks to Dean McGee) with a better mutation rate model then included.

I'm open for better (fast and easy) solutions.

ok, I have already modfied, back around 20110515, McGee's Utility reconfiguring to all 111 markers and replace Custom_MutRate with Burgarella2010 Rates else I used a 0.002 rate.

I am intending to use Marko Heinila newest rates in my modified version McGee's YDNA utility, which Ken Nordtvedt incorporated into his Gen111 TMRCA engine, which I modified MikeW's TMRCA Estimator spreadsheet. And I have read Marko's methods where he has perfomed calculations in which the mutation rates are scaled (or "calibrated") so that the expected number of mutations in the YHRD reported transmissions matches the actual observation.

MJost

ChrisR
12-03-2012, 12:56 PM
ok, I have already modfied, back around 20110515, McGee's Utility reconfiguring to all 111 markers and replace Custom_MutRate with Burgarella2010 Rates else I used a 0.002 rate.
Yeah, I know that. I have put an online version here:
http://y-dna-j-m304.gen.or.at/archive/Tools/McGee_Y-Utility_Comparison-111_Markers_Mod-MJost-Nov2011.HTM


I am intending to use Marko Heinila newest rates in my modified version McGee's YDNA utility, which Ken Nordtvedt incorporated into his Gen111 TMRCA engine, which I modified MikeW's TMRCA Estimator spreadsheet. And I have read Marko's methods where he has perfomed calculations in which the mutation rates are scaled (or "calibrated") so that the expected number of mutations in the YHRD reported transmissions matches the actual observation.
As Dean McGee has done an update on this tool in July 15, 2012
http://www.mymcgee.com/tools/yutility111.html
it would be interesting if you can share your additional coding with him to eventually merge the codebase and have an optimized online tool for all researchers. I respect Marko Heinila's STR-calculations's as one of the most informative out there. Looking forward for your new release.