====== Merlin ======
Merlin is a program from the [[http://www.sph.umich.edu/csg/abecasis|Abecassis Lab]] at the Center for Statistical Genetics, University of Michigan.

Its used for parametric and non-parametric linkage analysis in diploid populations.  Its algorithms utilise a sparse 'tree' for representing gene flow within pedigrees and its is particularly well geared towards handling dense marker maps.  There are a wide range of options to choose from when analysing your data and when used in conjunction with SimWalk2 provides a powerful set of tools for analysing your data.

Since its first release the functionality of Merlin has improved and it now handles dense genetic maps where [[linkage disequilibrium]] exists between markers, which if properly accounted for can increase the power to detect linkage.

===== Ebuild =====
The ebuild is shown below
<code python>
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $

DESCRIPTION="Statistical analysis of human pedigree data."
HOMEPAGE="http://www.sph.umich.edu/csg/abecasis/Merlin/"
SRC_URI="http://www.sph.umich.edu/csg/abecasis/Merlin/download/${P}.tar.gz"
SLOT="0"

# License of the package.  This must match the name of file(s) in
# /usr/portage/licenses/.  For complex license combination see the developer
# docs on gentoo.org for details.
LICENSE=""

KEYWORDS="~x86"

src_install() {
        mkdir ${D}usr #For some reason this is needed
        make install INSTALLDIR=${D}usr/bin || die
}
</code>

{{:merlin-1.1.2.ebuild.bz2|merlin-1.1.2.ebuild}}

===== Installation instructions =====
Create a directory in your ''/usr/local/portage'' overlay, grab the ebuild, digest it and emerge it

<code bash>
# mkdir -p /usr/local/portage/sci-biology/merlin
# cd /usr/local/portage/sci-biology/merlin
# wget http://kimura.no-ip.org/dokuwiki/lib/exe/fetch.php?id=merlin&cache=cache&media=merlin-1.1.2.ebuild.bz2
# bunzip2 merlin-1.1.2.ebuild.bz2
# ebuild merlin-1.1.2.ebuild digest
# emerge -av merlin
</code>

===== References ======

  * Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002). Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. //Nature Genetics// **30**:91-101 [[http://www.ncbi.nlm.nih.gov/pubmed/11731797|PubMed]][[http://www.sph.umich.edu/csg/abecasis/publications/pdf/Nat.Genet.vol.30-pp.97.pdf|full article]]
  * Sham PC, Purcell S, Cherny SS and Abecasis GR (2002) Powerful regression-based quantitative-trait linkage analysis of general pedigrees. //American Journal of Human Genetics// **71**:238-53 [[http://www.ncbi.nlm.nih.gov/pubmed/12111667|PubMed]][[http://www.sph.umich.edu/csg/abecasis/publications/pdf/Am.J.Hum.Genet.vol.71-pp.238.pdf|full article]]
  * Abecasis GR and Wigginton JE (2005) Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. //American Journal of Human Genetics// **77**:754-67 [[|PubMed]] [[http://www.sph.umich.edu/csg/abecasis/publications/pdf/Am.J.Hum.Genet.vol.77-pp.754.pdf|full article]]

===== Links =====
  * [[http://www.sph.umich.edu/csg/abecasis/merlin/|Merlin homepage]]
  * [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/|Merlin Tutorial]]
  * [[http://www.sph.umich.edu/csg/abecasis/|Abecasis Lab]]
  * [[http://www.sph.umich.edu/csg/|Ceneter for Statistical Genetics, University of Michigan]]