AINV                     (Animal Breeder's Tool Kit)                 AINV



NAME

     ainv - compute inbreeding coefficients and inverse numerator

          relationship matrix



SYNOPSIS

     ainv [-z] (pedigree file)



DESCRIPTION

     ainv computes  the inverse numerator relationship matrix and

     inbreeding coefficients for the population described  by the

     input pedigree  file.  The  pedigree file should  consist of

     three     columns:    individual     identification,    sire

     identification  and dam  identification, with  a record  for

     every individual  in the population.  The pedigree file must

     be constructed so that  every parent preceeds its offspring.

     Every  parent  must  also  have an  individual  record,  and

     unknown parent(s) must be indicated with a period (.).  



     If  the subdirectories  a_inverse  and scratch_files  do not

     exist  in  the current  directory,  ainv  will create  them.

     Files of  interest  created by  ainv are  inbred.lst in  the

     current  directory,  and v  in  the  a_inverse subdirectory.

     inbred.lst  is  a  list   of  the  pedigree  and  inbreeding

     coefficient  of all  individuals  in the  population with  a

     non-zero inbreeding coefficient.  a_inverse/v is the  SPARSE

     storage representation of the inverse numerator relationship

     matrix of the population.  



     ainv reports the  completion of each step  required to build

     the  inverse  numerator  relationship  matrix   to  standard

     output.  ainv builds a number of setup files, located in the

     scratch_files subdirectory, and the  ijdlist.dat file in the

     a_inverse  subdirectory.    The  file  a_inverse/ijdlist.dat

     contains  inverse  numerator relationship  matrix components

     before accumulation into a_inverse/v.   This file may become

     extremely  large  for sizeable  populations,  so  -z may  be

     specified to compress a_inverse/ijdlist.dat.   The files  in

     scratch_files  and  ijdlist.dat[.Z]  may  be  removed  after

     successful completion of ainv.  



     The algorithms used by ainv to compute the inverse numerator

     relationship   matrix   and   inbreeding  coefficients   are

     described by Golden et al. (1991).



EXAMPLE

     ainv -z hped91.ord



     Negative  inbreeding  coefficients  in  the  inbred.lst file

     indicates  the input pedegree file  is out of  sort order or

     not  sortable ascending.   See  stack_ped and  ped_recode to

     correct.

          

SEE ALSO

     chkord, ped_recode, stack_ped

     Golden, B.  L., J. S.  Brinks and R. M.  Bourdon.  1991.   A

         performance    programmed  method  for computing  inbreeding

         coefficients from large data sets  for  use  in mixed  model

         analyses.  J. Anim. Sci. 69:3564-3573.