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Subject: Inbreeding coefficient from a pedigree

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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