/************************************************************************
 * EMIM and PREMIM, version 3.22
 * Copyright 2012-2015,
 * Heather Cordell and Richard Howey
 * Institute of Human Genetics, Newcastle University
 *
 * firstname.lastname@ncl.ac.uk
 * http://www.staff.ncl.ac.uk/firstname.lastname/
 *
 * These programs are free software: you can redistribute them and/or modify
 * them under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * These programs are distributed in the hope that they will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along these programs.  If not, see <http://www.gnu.org/licenses/>.
 ************************************************************************/

For full details on how to install and use EMIM and PREMIM please read the documentation file:

emim.pdf

This documentation is based on the webpage for EMIM and PREMIM which you are adised to use as it may be more up to date:

http://www.staff.ncl.ac.uk/richard.howey/emim/


For details concerning the methodology of the multinomial likelihood approach used by EMIM, please see the accompanying manuscript Ainsworth et al. (2011):

Ainsworth HF, Unwin J, Jamison DL and Cordell HJ (2011) "Investigation of maternal effects, maternal-foetal interactions and parent-of-origin effects (imprinting), using mothers and their offspring" (Genet Epid 35:19-45).

Please also cite the following paper when reporting results using EMIM:

Howey R and Cordell, H J.
PREMIM and EMIM: Tools for estimation of maternal, imprinting and interaction effects using multinomial modelling.
BMC Bioinformatics, 13:149, 2012

If you make use of the extended version of EMIM to estimate the parent-of-origin using SHAPEIT2 then please cite the following paper:

Howey R and Cordell, H J.
Increased power of parent-of-origin (imprinting) effects using haplotype estimation
Publication pending, 2015


Files included with this distribution of EMIM and PREMIM include:

README.txt  -- This file
emim.pdf  -- Documentation for EMIM and PREMIM
gpl.txt -- GNU General Public License version 3

testpedigree.ped -- example pedigree file for PREMIM with 1 SNP and 130 pedigrees
testpedigree.map -- example map file for PREMIM with 1 SNP

emimparams.dat  -- example parameter file for EMIM
emimmarkers.dat -- example marker file for EMIM with 8 SNPs

Example genotype data files for use with EMIM with 8 SNPs:
caseparenttrios.dat
caseparents.dat
casemotherduos.dat
casefatherduos.dat
casemothers.dat
casefathers.dat
cases.dat
conparents.dat
conmotherduos.dat
confatherduos.dat
cons.dat

Source code files:
emim.f
maxfun.f
main.h
main.cpp
Data.h
Data.cpp
ProcessData.h
ProcessData.cpp
gzstream.h
gzstream.c



