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--- readme.inbupgf90 [2014/10/22 14:37] – [Calculation of inbreeding and relationship coefficients for specific animals/matings] ignacio
+++ readme.inbupgf90 [2024/03/25 18:22] (current) – external edit 127.0.0.1
@@ Line 27: / Line 27: @@
 ===== Optional command arguments =====
-<file>--alpha_size <n></file>
+<file>--help</file>
-change the maximun length of characters for alphanumeric Ids.\\
+print information of available arguments\\
+<file>--method <n></file>
+Several methods can be used:\\
+- recursive as in Aguilar & Misztal, 2008 \\
+- recursive but with coefficients stored in memory, faster with large number of generations but more memory requirements (default)\\
+- method as in Meuwissen & Luo 1992
-<file>--fmt <fmt></file>
-to read pedigree file with fixed format. Variables are assumed to be alphanumeric, e.g. '' '(3a8)' ''
 <file>--yob</file>
@@ Line 50: / Line 54: @@
 default is 1 i.e. zero inbreeding for individuals with missing parents.
-<file>--method <n></file>
+<file>--alpha_size <n></file>
-Several methods can be used:\\
+change the maximun length of characters for alphanumeric Ids.\\
- - recursive as in Aguilar & Misztal, 2008 (default)\\
-- recursive but with coefficients store in memory, faster with large number of generations but more memory requirements\\
+<file>--fmt <fmt></file>
-- method as in Meuwissen & Luo 1992
+to read pedigree file with fixed format. Variables are assumed to be alphanumeric, e.g. '' '(3a8)' ''
 ===== Misc =====
 <file>--prnrenped</file>
-using this option the renumber pedigree (parents Id precede their progeny Id) will be printed to a file.\\
+with this option, a renumbered pedigree (where parent ID precedes their progeny ID) will be printed to a file. If any, pedigree loops will be removed from this file.\\
-Inbreeding coefficients are not calculated !!!
+Inbreeding coefficients are not calculated!!!
@@ Line 67: / Line 72: @@
 Only inbreeding for required animals will be calculated!!
-<file>--sfile <SireFile></file>
+<file>--sire_file <SireFile></file>
 indicate the name of a file that contains a list of ''nsire'' individuals to be used as 'sires'
-<file>--dfile <DamFile></file>
+<file>--dam_file <DamFile></file>
 indicate the name of a file that contains a list of ''ndam'' individuals to be used as 'dams'
@@ Line 85: / Line 90: @@
 <file>--nrmcoeff_list <ListFile></file>
-statistic relationship information between all individuals in ListFile were calculated and  printed out in a file "ListFile.nrmcoeff"
+statistics of relationship information between all individuals in ListFile were calculated and printed out in a file "ListFile.nrmcoeff"
 format of file is Id_i, Id_j, relationship coefficient
 ===== Example =====