Abstract FAMOZ (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant and uniparentally inherited markers. It is written in C and TclTk languages and is available for Unix, Linux and Windows systems at http://www.pierroton.inra.fr/ genetics/labo/Software/Famoz/index.html. Parameters and assumptions used in the calculations are few and simple. Exclusion and identity probabilities, log-likelihoods of any genetic relationship, potential father and parent or parent pair, half-and full-sibship are calculated based on real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations can be done to build statistical tests for parentage assignment

A K R E M E R

Blackwell Publishing

P C H A B R I E R

S G E R B E R

CiteSeerX

 
Molecular Ecology Notes (2003) 
 
3
 
, 479–481 doi: 10.1046/j.1471-8286.2003.00439.x
© 2003 Blackwell Publishing Ltd
 
Blackwell Publishing Ltd.
 
PROGRAM NOTE
 
famoz
 
: a software for parentage analysis using dominant, 
codominant and uniparentally inherited markers
 
S .  GERBER,* P .  CHABRIER† and A.  KREMER*
*
 
INRA, UMR BIOGECO, 69 route d’Arcachon, 33612 Cestas cedex, France, 
 
†
 
INRA, Unité de biométrie et intelligence artificielle, 
Chemin de Borde-Rouge, Auzeville, BP 27, F-31326 Castanet-Tolosan cedex, France
 
Abstract
 
FAMOZ
 
 (an acronym for father/mother) is a software useful in reconstructing parentage for dom-
inant, codominant and uniparentally inherited markers. It is written in C and TclTk languages
and is available for Unix, Linux and Windows systems at http://www.pierroton.inra.fr/
genetics/labo/Software/Famoz/index.html. Parameters and assumptions used in the calcula-
tions are few and simple. Exclusion and identity probabilities, log-likelihoods of any genetic
relationship, potential father and parent or parent pair, half- and full-sibship are calculated
based on real or simulated data. Error rates for genotypic mistyping can be introduced.
Simulations can be done to build statistical tests for parentage assignment.
 
Keywords
 
:
 
 
 
LOD scores, open code software, paternity, simulation 
 
Received 6 March 2002; revision received 8 May 2002; accepted 10 March 2003
 
There is a growing interest in the study of gene flow. Most
of the studies use codominant markers, and especially micro-
satellites, to infer gene flow by parentage reconstruction.
However, we recently demonstrated that multiple dominant
markers could be used for the same purpose (Gerber 
 
et al
 
.
2000).
When several loci and many potential parents are
available, parentage assignment is based on statistical tests,
especially when both parents have to be identified. Meagher
& Thompson (1986) proposed likelihood methods to infer
parentage with codominant markers. We extended their
approach more recently to dominant markers (Gerber 
 
et al
 
.
2000). The existing software packages deal mostly with
paternity inference (Marshall 
 
et al
 
. 1998); our aim was to build
a more general frame for male and female assignment
including calculations based on codominant, dominant
and also cytoplasmic markers. As cytoplasmic markers are
uniparentally inherited, they may be helpful in inferring
the male or female origin once parentage analysis has iden-
tified the parent pair. We provide an open source compu-
ter software called 
 
famoz
 
, an acronym for father/mother
(http://www.pierroton.inra.fr/genetics/labo/Software/
Famoz/index.html). Source codes are sent on request. The
parameters and hypotheses used are few and basic. The
ability of a marker system to be used in parentage analysis
can be characterized with exclusion and identity probabil-
ities, expected according to allele frequencies or observed
in the sample. ‘Log of the odds ratio’ (LOD) scores are cal-
culated for any parentage relationship (potential father,
single parent or parent pairs). An error rate for genotypic
mistyping can be introduced and the package also tolerates
missing data. Simulations can be done by generating off-
spring from the genotyped parents or simply from allele
frequencies in the population. The simulations can be used
to build statistical tests for parentage assignment. The test
can also be applied to simulated samples to evaluate true,
apparent and cryptic gene flow.
 
Computer languages and tools
 
famoz
 
 is a program written in TclTk (ToolCommand-
Language/ToolKit; http://dev.scriptics.com/software/
tcltk/; Welch 1999), an easy to use, noncompiled scripting
language associating C programs. It provides the user with
a window and menus environment to handle files and
procedures involved in parentage analysis. Results are
given in a simple text format. Blt (http://sourceforge.net/
projects/blt/) is used for graphical purposes. Both TclTk
and Blt are freely distributed and run on platforms
including Unix, Linux, Macintosh and Windows.
Calculation codes (C language) were derived with
extensive modifications from programs written by E.
 
Correspondence: S. Gerber. Fax: (33) 5 57 12 28 81; E-mail:
gerber@pierroton.inra.fr
 
480
 
P R O G R A M  N O T E
 
© 2003 Blackwell Publishing Ltd, 
 
Molecular Ecology
 
 
 
Notes
 
, 3, 479–481
 
Thompson, available at ftp://ftp.u.washington.edu/pub/
user-supported/pangaea/PANGAEA/BOREL/estirel_96.Z.
These programs can be compiled with the GCC compilers
present on Unix and Linux platforms and freely available
for Windows (http://www.delorie.com/djgpp/).
Random numbers for simulations were generated
according to the method of Knuth (Press 
 
et al
 
. 1992).
 
Hypotheses, parameters and data sets
 
The parentage analysis available in 
 
famoz
 
 was originally
developed for forest trees and is thus based on an open
population for which only a subset of individuals is
genotyped (the trees of the study stand). The data from
‘inside the study stand’ correspond to the potential parents
that have been genotyped at the marker loci. The parents
from ‘outside the study stand’ are unknown. The relation-
ships that can be tested with the software include father/
offspring, father/mother/offspring and half- or full-
sibship (only for codominant markers).
The basic hypotheses used in the calculations are the
following:
 
1
 
loci are independently inherited according to Mendelian
laws;
 
2
 
cytoplasmic markers are considered fully uniparentally
inherited (either paternal or maternal);
 
3
 
allele frequency estimates are considered to be the true
allele frequencies;
 
4
 
the population is in panmixia; and
 
5
 
allelic frequencies ‘outside the study stand’ are assumed
to be the same as ‘inside the study stand’.
In addition, the user can introduce the following
restrictions:
 
1
 
The proportion of typing errors both in simulation and
in LOD score calculation. As mistyping is very likely to
occur, it is important that it be considered.
 
2
 
The departure from Hardy–Weinberg proportions,
Wright’s fixation index F, in the range [0,1]. When the
user provides a non-null value in simulations, homo-
zygous genotypes at any locus are more likely to be
obtained than by chance.
 
Exclusion probabilities
 
Exclusion probabilities are computed in 
 
famoz
 
 for
codominant (Jamieson & Taylor 1997) and dominant
markers (Gerber 
 
et al
 
. 2000).
Expected or observed identity probabilities represent
the probability that two individuals drawn at random or
observed from a population will have the same genotype
at multiple loci (Waits 
 
et al
 
. 2001).
 
‘Log of the odds ratio’ scores
 
Likelihood ratio or LOD scores are calculated for any
potential parentage relationship (father/parent/parent
pair) with a value greater than zero (Gerber 
 
et al
 
. 2000). The
higher the LOD score for a given parent/offspring pair, the
higher the likelihood that the parentage relationship is
true. Missing data are considered by the software. For
cytoplasmic data, the probability of an individual being
the true parent of a given offspring is simply 1 if they share
the same allele at the cytoplasmic marker (and 0 if they do
not share it), divided by the probability that this allele was
transmitted by another individual of the population
(frequency of this allele).
Since statistical laws associated to the likelihood ratio
test are unknown, we used simulations to calculate the thresh-
old values of the LOD score for parentage assignment.
 
Simulations
 
In 
 
famoz
 
, the simulations for paternity or parentage
analysis are designed for either ‘inside’ or ‘outside the
study stand’ and are built as follows:
 
1
 
randomly sampling a mother and father, generating a
gamete from the mother and father or randomly gener-
ating one or two gametes from the allele frequencies of
the data;
 
2
 
associating both gametes to generate the offspring; and
 
3
 
identifying the most likely father/parent/parent pair of
this offspring among the genotyped parents, recording
its LOD score value.
For each simulation the user chooses:
 
1
 
the number of simulated offspring;
 
2
 
the simulation error rate, i.e. the proportion of times a mis-
take will be made in simulations, replacing the allele from
the genotyped parents by a randomly selected one; and
 
3
 
the error rate used in LOD score calculation (Gerber 
 
et al
 
.
2000).
After the simulations, the two distributions of the LOD
score values (‘inside’/‘outside the study stand’) can be
compared. The intersection of the distributions can be used
to determine a threshold with known first and second type
errors. Since this rule can be too severe in some experimental
cases, the threshold can also be based solely on the distri-
butions of LOD scores corresponding to ‘inside the stand’.
 
Simulating individuals
 
famoz
 
 can simulate individuals for adding fictitious obser-
vations to data sets or for simulating additional loci. If 
 
n
 
P R O G R A M  N O T E
 
481
 
© 2003 Blackwell Publishing Ltd, 
 
Molecular Ecology Notes
 
, 3, 479–481
 
loci are available in the data set and the user wants 
 
m
 
 
 
≤
 
 
 
n
 
new loci, the software randomly simulates two gametes for
each new individual, drawing alleles according to the
frequencies of the 
 
n
 
 existing loci, starting from the first one
to the number 
 
m
 
. The simulated genotypes are eventually
provided to the user.
 
Testing data
 
Single parent and parent pair thresholds are provided by
the user. If a parent has an LOD score exceeding the single
parent threshold, it is considered as a true potential parent.
If a parent pair has an LOD score greater than the threshold
and comprises two true potential parents, it is considered
as a true potential parent pair (Meagher & Thompson
1986). 
 
famoz
 
 indicates the number of inferred parents
according to the test.
 
Simulation of paternity/parentage test: decisions 
and gene flow
 
The test built in the preceding step can be applied to simulated
data to measure their quality. To do so, the user chooses:
 
1
 
the number of mothers, selected either at random or in a
list for paternity analysis;
 
2
 
the number of simulated offspring;
 
3
 
the total number 
 
N
 
 of individuals participating in the
next generation. A [1,
 
N
 
] number is randomly generated.
If 
 
N
 
 is smaller than 
 
G
 
, the number of genotyped parents,
the father is selected among the individuals ‘inside the
stand’, otherwise the male gamete is generated accord-
ing to allele frequencies; and
 
4
 
the thresholds of the LOD scores.
Parentage assignment is made according to the test and
compared with the true situation and the number of cor-
rect assignments is recorded.
The following data about gene flow events are then
computed.
 
1
 
The expected gene flow: the proportion of gametes not
issued from the genotyped individuals, assuming equal
success rate among genotyped and nongenotyped indi-
viduals: (
 
N
 
 
 
−
 
 
 
G
 
)/
 
N
 
 
 
×
 
 total number of gametes.
 
2
 
The true gene flow: the actual number of times a gamete
generated according to allele frequencies (from ‘outside
the study stand’) produced one of the offspring.
 
3
 
The apparent gene flow: the number of times no parent
from ‘inside the study stand’ was detected for the simu-
lated offspring according to the statistical tests.
 
4
 
The cryptic gene flow: the number of times a parent was
detected among the genotyped parents according to the
statistical tests whereas the true parent was ‘outside the
study stand’.
 
Half- and full-sibship
 
The half- and full-sibship likelihood ratio for any pair of
individuals can be computed with 
 
famoz
 
 codominant
markers (Brenner 1997; http://dna-view.com/sibfmla.htm).
Simulations can be computed to build statistical tests for
measuring their ability to make correct decisions.
 
famoz
 
 reconstructs parent/offspring relationships based
on genotypic arrays obtained with different markers (dom-
inant or codominant, biparental and uniparental inherited)
or with a combination of markers. Other available soft-
wares are usually limited to paternity analysis and, to our
knowledge, there is none available using dominant and
uniparentally inherited markers. The few assumptions and
parameters required by the program make the results easy
to obtain and to understand. Other programs often require
more parameters that are not always easy to obtain for the
species studied. 
 
famoz
 
 can be used on any type of platform
and is freely available. The template of the program can
easily be used to create other specific programs.
 
Acknowledgements
 
We are very indebted and grateful to Georges Koepfler for his help
in C programming. The help of Frédéric Austerlitz, Sylvie Oddou-
Muratorio, Mathieu Lourmas, François Lefèvre and Clare Lord is also
acknowledged. This project has been supported by a European
project (OAKFLOW, QLK5-CT-2000-00960) and a national pro-
ject (2000–2002) supported by BRG (Genetic Resources Board)/
DERF (Rural Space and Forest Direction, French Ministry of
Agriculture).
 
References
 
Brenner CH (1997) Symbolic kinship program. 
 
Genetics
 
, 
 
145
 
, 535–
542.
Gerber S, Streiff R, Bodénès C, Mariette S, Kremer A (2000)
Comparison of microsatellites and AFLP markers for parentage
analysis. 
 
Molecular Ecology
 
, 
 
9
 
, 1037–1048.
Jamieson A, Taylor SS (1997) Comparisons of three probability
formulae for parentage exclusion. 
 
Animal Genetics
 
, 
 
28
 
, 397–
400.
Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical
confidence for likelihood-based paternity inference in natural
populations. 
 
Molecular Ecology
 
, 
 
7
 
, 639–655.
Meagher TR, Thompson E (1986) The relationship between single
parent and parent pair genetic likelihoods in genealogy recon-
struction. 
 
Theoretical Population Biology
 
, 
 
29
 
, 87–106.
Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1992)
Random numbers. In: 
 
Numerical Recipes in C: the Art of Scientific
Computing
 
, pp. 274–286. Cambridge University Press, Cambridge.
Waits LP, Luikart G, Taberlet P (2001) Estimating the probability
of identity among genotypes in natural populations: cautions
and guidelines. 
 
Molecular Ecology
 
, 
 
10
 
, 249–256.
Welch B (1999) 
 
Practical Programming in Tcl and Tk
 
, 3rd edn.
Prentice Hall, Upper Saddle River, NJ.


famoz : a software for parentage analysis using dominant, codominant and uniparentally inherited markers

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famoz : a software for parentage analysis using dominant, codominant and uniparentally inherited markers

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