From koreaheart_at_hotmail.com Wed Oct 19 18:24:19 2005 From: "shin hun kim" <koreaheart_at_hotmail.com> Subject: Inbreeding coefficient from a pedigree Date: Wed, 19 Oct 2005 16:24:16 -0700 To: Multiple Recipients of <angenmap_at_animalgenome.org> Hello, I am studying Genetics in Animal science with Japanese Quail. I have to get inbreeding coefficient from their pedigree. What computer program would you recommend ? Moreover, in almost every mate,sires are mated to more than 2 (3,4,or 5), which means we don't know exactly where the next generation from of the dams. how should I go about it? Please anybody who knows about it teach me. Thanks, Shin Shin Hun Kim Master Degree student Genetics Graduate Program University of British Columbia

From gregor.gorjanc_at_bfro.uni-lj.si Wed Oct 19 23:40:21 2005 Date: Thu, 20 Oct 2005 06:40:49 +0200 From: Gregor Gorjanc <gregor.gorjanc_at_bfro.uni-lj.si> Subject: Re: Inbreeding coefficient from a pedigree To: Multiple Recipients of <angenmap_at_animalgenome.org> shin hun kim wrote: > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Hello, > > I am studying Genetics in Animal science with Japanese Quail. I have to get > inbreeding coefficient from their pedigree. What computer program would you > recommend ? I do not use any GUI like program, althought there are some. I noticed publication for one in Journal of Animal Breeding and Genetics (2005) - program ENDOG, which can be accessed for free[1]. Please note that I have not tried it. Pedigree viewer[2] can also be easy and nice to use. I prefer console oriented programs. Pedig[3] is especially oriented towards pedigree "analysis". Additionally, one can other programs, which are not directly oriented to pedigree "analysis" but have possibility to output inbreeding coefficients: PEST[4], VCE[5], Matvec[6] and others. For recent development in computing inbreeding coefficients read Sargolzaei (2005)[7] and references therein. This Note that only PEST is not available for free from the list above. > Moreover, in almost every mate,sires are mated to more than 2 > (3,4,or 5), which means we don't know exactly where the next generation from > of the dams. how should I go about it? I am sorry but I do not understand you point here. Anyway, mentioned programs were developed with animal breeding data in mind, where one can find complex structures and I think at least one of them will suit your needs. [1] http://www.ucm.es/info/prodanim/Endog30.zip [2] http://www-personal.une.edu.au/%7Ebkinghor/pedigree.htm [3] http://www-sgqa.jouy.inra.fr/sgqa/diffusions/pedig/pedigE.htm [4] http://w3.tzv.fal.de/%7Eeg/ [5] http://vce.tzv.fal.de/index.pl [6] http://statistics.unl.edu/faculty/steve/software/matvec/ [7] _at_Article {Sargolzaei:2005, author = {Sargolzaei, M. and Iwaisaki, H. and Colleau, J.-J.}, title = {A fast algorithm for computing inbreeding coefficients in large populations}, journal = {J. Anim. Breed. Genet.}, year = {2005}, volume = {122}, number = {5}, pages = {325--331}, URL = {http://dx.doi.org/10.1111/j.1439-0388.2005.00538.x} } -- Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student Biotechnical Faculty Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan Groblje 3 mail: gregor.gorjanc bfro.uni-lj.si SI-1230 Domzale tel: +386 (0)1 72 17 861 Slovenia, Europe fax: +386 (0)1 72 17 888 ---------------------------------------------------------------------- "One must learn by doing the thing; for though you think you know it, you have no certainty until you try." Sophocles ~ 450 B.C. ----------------------------------------------------------------------

From i.aoultchenko_at_erasmusmc.nl Thu Oct 20 08:17:43 2005 Date: Thu, 20 Oct 2005 14:17:16 +0100 From: Yurii Aulchenko <i.aoultchenko_at_erasmusmc.nl> Subject: Re: Inbreeding coefficient from a pedigree To: Multiple Recipients of <angenmap_at_animalgenome.org> Hi Shin, PEDIG by Dieder Boichard is a very fast one, and free. Also contains module for kinship computations and many many other things. It got Win binaries. Available at http://dga.jouy.inra.fr/sgqa/diffusions/pedig/pedigE.htm best wishes, Yurii shin hun kim wrote: > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Hello, > > I am studying Genetics in Animal science with Japanese Quail. I have to get > inbreeding coefficient from their pedigree. What computer program would you > recommend ? Moreover, in almost every mate,sires are mated to more than 2 > (3,4,or 5), which means we don't know exactly where the next generation from > of the dams. how should I go about it? > > Please anybody who knows about it teach me. > > Thanks, > > Shin > > > Shin Hun Kim Master Degree student Genetics Graduate Program University of > British Columbia > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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