A. FILE LISTS
Makefile Compiles and links all programs
testg.sh Runs test data us GEMINI
testn.sh Runs test data us NPSOL
c1.inc Parameters and common used by preped
c123456.inc Parameters and common used by preped, descstat, prepap, simul, papdr, gpe
c1245.inc Parameters and common used by preped, descstat, simul, papdr
c12456.inc Parameters and common used by preped, descstat, simul, papdr, gpe
c13456.inc Parameters and common used by preped, prepap, simul, papdr, gpe
c145.inc Parameters and common used by preped, simul, papdr
c16.inc Parameters and common used by preped, gpe
c2345.inc Parameters and common used by descstat, prepap, simul, papdr
c245.inc Parameters and common used by descstat, simul, papdr
c3.inc Parameters and common used by prepap
c345.inc Parameters and common used by prepap, simul, papdr
c45.inc Parameters and common used by simul, papdr
c456.inc Parameters and common used by simul, papdr, gpe
c45d.inc Parameters and common used by simul, papdr
c45t.inc Parameters and common used by simul, papdr
c5.inc Parameter and common used by papdr
c5t.inc Parameter and common used by papdr
const.inc Constants used in simul, papdr
gemini.inc Parameters and common used by GEMINI
i1.inc Include files for preped
i1236.inc Include files for preped, descstat, prepap and gpe
i13456.inc Include files for preped, prepap, simul, papdr and gpe
i16.inc Include files for preped and gpe
i2.inc Include files for descstat
i245.inc Include files for descstat, simul, and papdr
i3.inc Include files for prepap
i345.inc Include files for prepap, simul and papdr
i35.inc Include files for prepap and papdr
i4.inc Include files for simul
i45.inc Include files for simul and papdr
i45d.inc Include files for simul and papdr
i45t.inc Include files for simul and papdr
i5.inc Include files for papdr
i5t.inc Include files for papdr
i6.inc Include files for gpe
papch.inc I/O logical unit numbers
alloff.f Determines alleles in descendants of an individual untyped for a marker
assort.f Iterates to find equilibrium genotype and mating frequencies
chkbnd.f Checks boundary conditions for GEMINI
confun.f Defines the nonlinear constraints for NPSOL
daterr.f Error messages for preped, descstat, simul, papdr, gpe
datin.f Reads in data files for simul and papdr
descstat.f Computes descriptive statistics from papin.dat
devia.f Locates the normal deviation corresponding to a specified probability
dmlpr0.f Dummy subroutine used when no discrete traits are included
dmlprin.f Converts incidence figures to normal deviates and assigns age categories
dmlprpn.f Converts penetrances to normal deviates
dmlprpr.f Converts prevalence figures to normal deviates and assigns categories
dmlprsv.f Converts prevalence for severity designations to normal deviates
domdis.f Translates dominance and displacement into genotypic means and a common standard deviation
drand.c Call random number generator
filerr.f Prints error messages for preped, descstat, prepap, simul, papdr, gpe
genot.f Outputs the alleles comprising a particular genotype
gpe.f Estimates frequencies, genotypic means using the genotypic probabilities
iallel.f Determines alleles by locus
igenlc.f Determines genotypes by locus
igtrat.f Determines genotypes by trait
inib.f Obtain initial approximation to Hessian for GEMINI
inmin.f Interactive input of an integer, checking bounds
integ.f Computes the normal integral below a specified point
moderr.f Prints error messages for descstat, prepap, simul, papdr
modin.f Reads model information and parameter values from model.dat
modnew.f Queries the user for input for model.dat
modot.f Writes model information and parameter values to model.dat
objfun.f Returns log likelihood values to NPSOL
papcl.f Calculates the likelihood of children in a nuclear family
papcr.f Dummy subroutine used when no within genotype correlations
papcrda.f For discrete traits, corrects approximation for genotype
papcrde.f Penetrance for discrete traits and the exact mixed model
papcrdqa.f For discrete or quantitative traits, corrects approximation for genotype
papcrdqe.f Penetrance for discrete or quantitative traits and the exact mixed model
papcrqa.f For quantitative traits, corrects approximation for genotype
papcrqe.f Penetrance for quantitative traits and the exact mixed model
papcsg.f Simulates genotypes conditionally and assigns phenotypes
papcsg0.f Dummy subroutine used in simul
papdr.f Driver of the analysis program
papel.f Computes expected lod scores for pedigrees
papen.f Dummy subroutine used when no traits are included
papend.f Penetrance for discrete traits and major locus model
papenda.f Penetrance for discrete traits and the approximate mixed model
papende.f Penetrance for discrete traits and exact mixed model
papendq.f Penetrance for discrete/quantitative traits and major locus model
papendqa.f Penetrance for discrete or quantitative traits and the approximate mixed model
papendqe.f Penetrance for discrete/quantitative traits and exact mixed model
papenq.f Penetrance for quantitative traits and major locus model
papenqa.f Penetrance for quantitative traits and the approximate mixed model
papenqe.f Penetrance for quantitative traits and exact mixed model
paperr.f Prints error message for simul and papdr
papes.f Simulates phenotypes and estimates parameters
papfqa2.f Autosomal genotype frequencies computed from conditional allele frequencies at the first locus and unconditional allele frequencies at the second locus
papfqa2s.f Category-specific autosomal genotype frequencies computed from conditional allele frequencies at the first locus and unconditional allele frequencies at the second locus
papfqg.f Genotype frequencies stored
papfqh.f Genotype frequencies computed from haplotype frequencies assuming Hardy-Weinberg equilibrium
papfqh2.f Genotype frequencies computed for two autosomal loci allowing for linkage disequilibrium
papfqhw.f Genotype frequencies computed from allele frequencies assuming Hardy-Weinberg equilibrium and linkage equilibrium
papfqx2.f Genotype frequencies computed for two X-linked loci allowing for linkage disequilibrium
papfqxa.f Genotype frequencies computed for the autosomal/X-linked model
papgd.f Computes likelihoods for a grid of parameter values
papgn.f Stores genotype and alleles by locus and trait for the model
papgp.f Genotypic probability routine
paplk.f Computes the likelihood on a pedigree or the sample
papmv.f Determines possible genotypes and indistinguishable genotypes for each individual untyped for a marker
papmv0.f Dummy subroutine for use by simul
papmxg.f Maximizes the likelihood using GEMINI
papmxn.f Maximizes the likelihood using NPSOL
papnf.f Computes the likelihood of one nuclear family
pappd.f Computes the likelihood of a pedigree considering all genotype sets
pappg.f Determines possible genotypes for pedigree members
pappl.f Computes the likelihood of one pedigree
pappn.f Computes the penetrance for each individual in a pedigree
pappo.f Outputs the parameter values to the screen and pap.out
pappr.f Computes the probability of each genotype for an individual
papro.f Outputs the results from papdr
papse.f Computes standard errors
papsf.f Calls papsg to simulate phenotypes and writes the phenotypes in files
papsg.f Simulates genotypes and assigns phenotypes
papsm.f Adds two numbers, each stored as logs
paptcal.f Computes transmission probabilities for autosomal linkage
paptcapl.f Computes transmission probabilities for parent-specific autosomal linkage
paptcasl.f Computes transmission probabilities for category-specific linkage
paptcaxl.f Computes transmission probabilities for autosomal/X-linked admixture
paptce.f Stores genotype frequencies as transmission probabilities
paptcet.f Computes transmission probabilities from parameters assuming generational equilibrium
paptcms.f Transmission probabilities for Mendelian segregation and no linkage
paptctp.f Computes transmission probabilities from parameters
paptcxl.f Computes transmission probabilities for X-linked inheritance
paptcxpl.f Computes transmission probabilities for parent-specific X-linked inheritance
paptr.f Transfers parameter values from the maximization array into the appropriate names
papwg.f Dummy subroutine used when no traits are included
papwgfc.f Produces the correlation matrix from specified familial correlations
papwgml.f Produces the correlation matrix assuming no within-genotype correlation
papwgvc.f Produces the correlation matrix from variance components
parin.f Queries the user for input for model.dat
parnew.f Reads in parameter values and boundaries
pedgen.f Assembles father, mother, offspring triples into pedigrees
pedin.f Reads papin.dat
pedot.f Outputs papin.dat
phenin.f Reads phen.dat
popin.f Reads popln.dat
prepap.f Produces model.dat through interactive input
preped.f Combines trip.dat, order.dat, header.dat, phen.dat, ascer.dat into papin.dat
pselec.f Lists variables for the user's selection
qmlpr0.f Dummy subroutine used when no quantitative traits are included
qmlprdd.f Converts dominance and displacement to genotypic means and variances
qmlprmv.f Stores the genotypic means and standard deviation
qmlprmvt.f Stores the genotypic means and standard deviation and computes a deviation corresponding to the threshold
repeat.f Calls alloff to make it recursive
rev3_4.f Converts peel.dat, phen.dat, marker.dat (Rev.3) to trip.dat, order.dat, header.dat, phen.rev4, ascer.dat, popln.dat (Rev.4)
rnmin.f Interactive input of a double precision number, checking bounds
sbrlib.f Reads the subroutine library files
simph.f Determines traits/markers and phenotypes to be simulated
simul.f Calls subroutines to simulates phenotypes and write them in files
step.f Performs line search for GEMINI
thresh.f Locates threshold corresponding to prevalence for multiple genotypes
update.f Updates matrix for GEMINI
yesno.f Interactive input of yes/no response
dmlp.dat Major locus for discrete traits subroutine library
freq.dat Frequency subroutine library
qmlp.dat Major locus for quantitative traits subroutine library
tran.dat Transmission subroutine library
wgen.dat Within genotype subroutine library
ascer.tst Phenotype data for probands
header.tst1 Variable names and characteristics
header.tst2 Variable names and characteristics
header.tst3 Variable names and characteristics
header.tst4 Variable names and characteristics
pap1.dat Interactive input for option 1
pap2.dat Interactive input for option 2
pap3.dat Interactive input for option 3
pap4.dat Interactive input for option 4
pap5.dat Interactive input for option 5
pap6.dat Interactive input for option 6
pap7.dat Interactive input for option 7
pap8.dat Interactive input for option 8
phen.tst Phenotype data
popln.tst Population marker information
preped.dat Interactive input for preped
preped2.dat Interactive input for preped
trip.tst Pedigree structure
m_1_1.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_1_2.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 2, responses y and y
m_1_3_1.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 3, responses 2 and 1
m_1_3_2.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 3, responses 2 and 1
m_1_4.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 4, responses n and n
m_1_5.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 5, response n
m_1_6.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 6, responses 2 and 1
m_1_7.dat papfqhw, paptcal, dmlpr0, qmlpr0, papwg, papen, papcr, option 7, responses 2 and 1
m_1_8.dat papfqhw, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 8, responses 2 and 1
m_2_1.dat papfqhw, paptctp, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_2_2.dat papfqhw, paptctp, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_2_3.dat papfqhw, paptctp, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_3_1.dat papfqhw, paptcal, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_3_2.dat papfqhw, paptcal, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_1_1.dat papfqh2, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_1_2.dat papfqh2, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_2_1.dat papfqa2, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_2_2.dat papfqa2, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_3_1.dat papfqh, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_3_2.dat papfqh, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_4_1.dat papfqg, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_4_4_2.dat papfqg, paptcms, dmlpr0, qmlpr0, papwg, papen, papcr, option 1
m_5_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_5_2.dat papfqhw, paptcms, dmlprpr, qmlpr0, papwgml, papend, papcr, option 1
m_5_3.dat papfqhw, paptcms, dmlprin, qmlpr0, papwgml, papend, papcr, option 1
m_5_4.dat papfqhw, paptcms, dmlprsv, qmlpr0, papwgml, papend, papcr, option 1
m_6_1.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgml, papenq, papcr, option 1
m_6_2.dat papfqhw, paptcms, dmlpr0, qmlprdd, papwgml, papenq, papcr, option 1
m_6_3.dat papfqhw, paptcms, dmlpr0, qmlprmvt, papwgml, papendq, papcr, option 1
m_7_1_1.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgvc, papenqe, papcrqe, option 1
m_7_1_2.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgvc, papenqe, papcrqe, option 1
m_7_2_1.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgvc, papenqa, papcrqa, option 1
m_7_2_2.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgvc, papenqa, papcrqa, option 1
m_7_3_1.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgfc, papenqa, papcrqa, option 1
m_7_3_2.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgfc, papenqa, papcrqa, option 1
m_8_1_1.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgml, papenq, papcr, option 1
m_8_1_2.dat papfqhw, paptcms, dmlpr0, qmlprmv, papwgml, papenq, papcr, option 1
m_8_2_1.dat papfqhw, paptcms, dmlprpn, qmlprmv, papwgml, papendq, papcr, option 1
m_8_2_2.dat papfqhw, paptcms, dmlprpn, qmlprmv, papwgml, papendq, papcr, option 1
m_9_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_2.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_3_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_3_2.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_4_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_4_2.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_5_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_5_2.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_6_1.dat papfqxa, paptctp, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_6_2.dat papfqxa, paptctp, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_6_3.dat papfqxa, paptctp, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_7_1.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_7_2.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
m_9_7_3.dat papfqhw, paptcms, dmlprpn, qmlpr0, papwgml, papend, papcr, option 1
papout.tst Results of running the test data