1 Introduction

According to Wikipedia, “Emim” was the Moabite name for one of the tribes of Rephaim. They are described in Deuteronomy chapter 2 as having been a powerful people, populous and having a successful kingdom. The Emim are also mentioned in Genesis 14:5 where the name is translated as “the dreaded ones”.

Hopefully our program EMIM will prove an equally powerful tool for the detection of complex effects in genetic disease studies...

1.1 Program information and citation

If you use the PREMIM/EMIM software in your work then please reference the accompanying software manuscript Howey and Cordell (2012):

@article{howey:cordell:12,
  author = {Howey, R and Cordell, H J},
  title = {{PREMIM} and {EMIM}: Tools for estimation of maternal, imprinting and interaction effects using multinomial modelling},
  journal = {{BMC} Bioinformatics},
  volume = {13},
  pages = {149},
  year = {2012}
}

For use of the methodology of the multinomial likelihood approach used by this program, please reference the accompanying manuscript Ainsworth et al. (2011):

@article{ainsworth:etal:11,
  author={Ainsworth, H F and Unwin, J and Jamison, D L and Cordell, H J},
  title = {Investigation of maternal effects, maternal-foetal interactions and parent-of-origin effects (imprinting), using mothers and their offspring},
  journal = {Genet Epidemiol},
  volume = {35},
  pages = {19-45},
  number = {1},
  month = {January},
  year = {2011}
}

You are STRONGLY recommended to read this paper before using EMIM in order to understand the notation and parameter restrictions/analysis options used.

If you have used PREMIM/EMIM to estimate parent-of-origin effects with the use of SHAPEIT2 to estimate the parent-of-origin of alleles, please reference Howey et al. (2015):

@article{howey:etal:15,
author={Howey, R and Mamasoula, C and T\"opf, A and Nudel, R and Goodship, J A and Keavney, B D and Cordell, H J},
title={Increased Power for Detection of Parent-of-Origin Effects via the Use of Haplotype Estimation},
journal={The American Journal of Human Genetics},
volume={97},
number={3},
pages={419-434},
year={2015}
}

EMIM is a FORTRAN 77 program with some FORTRAN 90 features and compiles under Linux or Windows (DOS) using a suitable compiler e.g. gfortran. We have not tried compiling on any other system, but see no reason why the program should not compile provided an appropriate FORTRAN compiler is available. To run EMIM under Windows, you will need to use the command line interface (i.e. open a command line (DOS) window).

EMIM uses a maximisation subroutine MAXFUN that was originally written as part of (a former early version of) the S.A.G.E. package: http://darwin.cwru.edu/sage/

Users of S.A.G.E are asked to insert the following acknowledgment in any publication that uses results obtained from S.A.G.E.:

“(Some of) The results of this paper were obtained by using the program package S.A.G.E., which is supported by a U.S. Public Health Service Resource Grant (RR03655) from the National Center for Research Resources” (it is important that the grant number appears under “acknowledgments”).

Please see more details on the S.A.G.E website: http://darwin.cwru.edu/sage/?q=node/5

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