An Alphabetic List of Genetic Analysis Software - Jurg Ott

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An Alphabetic List

of

Genetic Analysis Software




Last u
pdate
d
: 1
7 October

2012


Computer software on the following topics is included here: genetic linkage analysis for human
pedigree data, QTL analysis for
animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing,
and
population genetics. This list is offered here as a service to the gene mapping community. The
inclusion of a program should not
be interpreted as an endor
sement from us.

In the last few years, new technology
has been
produc
ing

new types of genetic data, and the scope of genetic analyses change
s

dramatically. It is no longer obvious whether a progra
m should be included or excluded from this list. Topics such as next
-
generation
-
sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study,

but we'll have to
decide on a case
-
by
-
case basis whether to include a progr
am

(
email us

if you are interested in having a program listed here)
.

This page was created by Dr.
Wentian Li
, when he was at Columbia University (1995
-
1996). It w
as later moved to Rockefeller
University (1996
-
2002) and now it takes its home at
North Shore LIJ Research Institute

(2002
-
now). The present copy is
maintained by
Jurg Ott

as a single file. More than 240 programs
were

listed by December 2004, close to 400 programs by
December 2006, close to 480 programs by November 2008, and
over 600

programs by
October

201
2
. A version of the searchable
database was developed by
Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of
Har
bin Medical School.

Some earlier software can be downloaded from EBI:
ftp://ftp.ebi.a
c.uk/pub/software/linkage_and_mapping/

(Linkage and
Mapping Software Repository), and
http://genomics.com/software/index.htm

may contain
archived copy of some programs.

More and more packages are now w
ritten in R. To be consistent, any R package in CRAN
has been

renamed from [package
-
name]
to R/[package
-
name]. If an R package is not submitted to CRAN, its original name has been kept. Here is another partial list of
statistical genetics R packages summar
ized by CRAN:
http://cran.r
-
project.org/web/views/Genetics.html
.
M
ore R packages

yet

can be found at:
http://www.mr
c
-
epid.cam.ac.uk/~jinghua.zhao/r
-
genetics.htm
,
http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
,
http://wpicr.wpic.pitt.edu/WPICCompGen/software.htm
,

http://www
-
gene.cimr.cam.ac.uk/clayton/software/
, a
nd

other places.




ACT

o

full name: Analysis of Complex Traits

o

version: 1.1 (Mar

17,

2000)

o

description: It contains the following modules: ibd, calculates the proportion of gene shared
identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a
method for assessing increased
-
allele sharing between al
l pairs of affected relatives within a
pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components
using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov,
generates first degree
relationship coefficients for extended families; sim2s, the simulation program
that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily
modified to assist multipoint calculation using multic; TDT: TDT programs writ
ten in SAS
;

gcc and f77
compilers are necessary. Executable programs are included for compatible operating system
s
, i.e.,
Solaris2.6.

o

authors: Christopher I. Amos (email: camos@request.mdacc.tmc.edu
)
, Mariza de Andrade (email:
mandrade@request.mdacc.tmc.edu
)
, JianFang Chen (email: cjf@request.mdacc.tmc.edu)

o

web/ftp: http://www.epigenetic.org/Linkage/act.html,
http://www.epigenetic.org/Linkage/act.tar.gz

o

source code language: FORTRAN77, C++

o

operating systems: UNIX(Solaris 2.4/..)

o

executables: ibd, ml, ql, he, ibdn, multic

o

reference: Amos, et al (1996), "Assessing genetic linkage and association with robust components of
variance approaches", Annals of Human Genetics, 60:143
-
160.

o

Amos (1994), "Robust variance
-
components approach fo
r assessing genetic linkage in pedigrees",
American Journal of Human Genetics, 54:535
-
543. [
abstract
]

o

de Andreade, Amos, Thiel (1999), "Methods to estimate genetic parameters

for quantitative traits",
Genetic Epidemiology, 17(1):64
-
76.



ADEGENET (see also R/ADEGENET
)



ADMIXMAP

o

full name: Admixture mapping

o

version: 3.7 (2007)

o

description: ADMIXMAP is a general
-
purpose program for modelling admixture, using marker
genotypes and tr
ait data on a sample of individuals from an admixed population (such as African
-
Americans), where the markers have been chosen to have extreme differentials in allele frequencies
between two or more of the ancestral populations between which admixture has
occurred. The
main difference between ADMIXMAP and classical programs for estimation of admixture such as
ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture
in the population and the stochastic variation of a
ncestry on hybrid chromosomes. This makes it
possible to model the associations of ancestry between linked marker loci, and the association of a
trait with individual admixture or with ancestry at a linked marker locus.

o

authors: Clive Hoggart, Nigel Wetter
s, David Clayton, David O'Donnell (email:
david.odonnell@ucd.ie), and Paul McKeigue (email: paul.mckeigue@ucd.ie)

o

web/ftp: http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

o

source code language: C++

o

operating systems: Linux, MS
-
Windows

o

executables
: admixmap, admixmap.pl, and some R scripts to process the output

o

reference: PM McKeigue (2005), "Prospects for admixture mapping of complex traits", American
Journal of Human Genetics, 76(1):1
-
7

o

CJ Hoggart, MD Shriver, RA Kittles, DG Clayton, PM McKeigue
(2004), "Design and analysis of
admixture mapping studies", American Journal of Human Genetics, 74(5):965
-
978

o

CJ Hoggart, EJ Parra, MD Shriver, C Bonilla, RA Kittles, DC Clayton, PM McKeigue (2003), "Control of
confounding of genetic associations in strati
fied populations", American Journal of Human Genetics,
72(6):1492
-
1504

o

PM McKeigue, J Carpenter, EJ Parra, MD Shriver (2000), "Estimation of admixture and detection of
linkage in admixed populations by a Bayesian approach: application to African
-
American
p
opulations", Annals of Human Genetics, 64:171
-
186.



AGEINF

o

full name:

o

version:

o

description: inference of the age of a rare, selectively
-
neutral mutation

o

authors: Jinko Graham

o

web/ftp: http://www.math.sfu.ca/~jgraham/Papers/Programs/AgeCode/

o

source code
language: C

o

operating systems:

o

executables:

o

reference: Graham, Thompson (2000), "A coalescent model of ancestry for a rare allele", Genetics,
156:375
-
384.



ALBERT

o

full name: A Likelihood Based Estimation of Risk in Trios

o

version: 1.0 (May 2006)

o

description:

ALBERT is a program that estimates genotype relative risks, genotyping error rates and
population risk allele frequencies from marker genotype data in case
-
parent trios. ALBERT uses the
distribution of trio marker genotypes to compute maximum likelihood e
stimates for the parameters.

o

authors: Adele Mitchell, Elizabeth A Thompson (University of Washington)

o

web/ftp: http://www.stat.washington.edu/thompson/Genepi/Albert/albert.shtml

o

source code language: C

o

operating systems: UNIX, Linux

o

executables:

o

reference:



ALLASS

o

full name:

o

version: February 2002

o

description:

o

authors: A Collins (email: arc@soton.ac.uk), NE Morton (University of Southampton, UK)

o

web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ALLASS

o

source code language: C

o

operating systems: UNIX

(SU
N..)

o

executables: allass

o

reference: Collins, Morton (1998), "Mapping a disease locus

by allelic association", Procee
dings of
the National Academy of Sciences , 95:1741
-
1745; online manual



ALLEGRO

o

full name:

o

version: 2.0 (October 2005)

o

description: a faster

version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed,
can handle bigger families, up to 50 bits)

o

authors: Daniel F Gudbjartsson, TA Thorvaldsson, G Gunnarsson, Augustine Kong, A Ingolfsdottir
(DeCode Genetics, Inc. Iceland) send ema
il to: allegro@decode.is

o

web/ftp: http://www.decode.com/software/

o

source code language: C++

o

operating systems:

o

executables:

o

reference: D Gudbjartsson, K Jonasson, CA Kong (1999), "Fast multipoint linkage calculation with
Allegro", American Journal of Human

Genetics, 65(suppl):A60.

o

Gudbjartsson, Jonasson, Frigge, Kong (2000) "Allegro, a new computer program for multipoint
linkage analysis", Nature Genetics, 25:12
-
13.

o

Gudbjartsson, Thorvaldsson, Gunnarsson, Kong, Ingolfsdottir (2004), "Decision diagram based
multipoint linkage analysis: ALLEGRO2", American Journal of Human Genetics, 75(suppl):?.

o

Gudbjartsson, Thorvaldsson, Kong, Gunnarsson, Ingolfsdottir (2005), "Allegro version 2", Nature
Genetics, 37:1015
-
1016. [
PLEASE CITE THIS REFERENCE WHEN USING THE ALLE
GRO2 PROGRAM
]



ALLELIX

o

full name: Allelix
-

Paternity Linkage Analysis Online

o

version: December 2001

o

description: One can enter the alleles of commonly used STR by clicking the mouse. The algorithm
calculates the paternity index and the Essen
-
Moeller probab
ility of kinship for the deficiency
-

and
the trio case. Everybody can use the network
-
software online after registering. The usage on the
internet is free. Academic users can ask me to unlock an option to display the details
(formulas/frequencies etc.) and

to have an export
-
funktion to MS Word. The program is in German
and (non
-
professional) English. An expansion to other languages is easy, if somebody helps us with
the translation. For those who are interested to have the software running on their own intr
anet (for
database security reasons) an individual agreement can be found.

o

authors: Thomas Krahn (biotix) (email: tk@biotix.de), Stefan Zinke (Software Erstellung
-

und
Beratung, Germany), Dr. Michael Kraft (biotix)

o

web/ftp: http://www.allelix.net (German v
ersion is: http://www.allelix.de)

o

source code language: C++, Java Script

o

operating systems: MS
-
Windows (2000 &IIS/ME & Personal Webserver)

o

executables: allelix.dll

o

reference:



ALOHOMORA

o

full name:

o

version: 0.33 (October 2009)

o

description: designed to facili
tate genome
-
wide linkage studies performed with high
-
density single
nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping
10K Array.

o

authors: Franz Ruschendorf (email: fruesch@mdc
-
berlin.de), Peter Nurnberg

o

web/ftp:
http://gmc.mdc
-
berlin.de/alohomora/

o

source code language: perl

o

operating systems: MS
-
Window, Linux, UNIX

(Solaris/..)

o

executables:

o

reference: Ruschendorf, Nu
rnberg (2005), "ALOHOMORA: a tool for linkage analysis using 10K SNP
array data", Bioinformatics, 2
1(9):2123
-
2125.



ALP

o

full name: Automated Linkage Preprocessor

o

version: v1.40 (August 1995)

o

description: ALP is a Microsoft Windows application designed to analyse microsatellite DNA
fragments separated on an Automated Laser Fluorescence sequencer.

o

authors:

Alastair Brown (email: alastair.brown@hgu.mrc.ac.uk), Daryll Green, Steve Woess (MRC
Human Genetics Unit, Edinburgh, UK).

o

web/ftp: http://www.hgu.mrc.ac.uk/Softdata/ALP/

o

ftp://ftp.hgu.mrc.ac.uk/pub/ALP

o

source code language: C

o

operating systems: MS
-
Windows

(3.1/95/NT)

o

executables: alpw.exe

o

reference: Mansfield, Brown, Green, Carothers, Morris, Evans, Wright (1994), "Automation of
genetic linkage analysis using fluorescent microsatellite markers", Genomics, 24(2):225
-
233.



ALTREE

o

full name:

o

version:

o

descripti
on: ALTREE performs these two phylogeny
-
based analysis: (1) it tests the association
between a candidate gene and a disease; (2) it pinpoints markers (SNPs) that are putative disease
susceptibility loci

o

authors: Claire Bardel (email: bardel@vjf.inserm.fr),

Vincent Danjean, Jean
-
Pierre Hugot, Pierre
Darlu, Emmanuelle Génin

o

web/ftp: http://claire.bardel.free.fr/software.html

o

source code language:

o

operating systems:

o

executables: altree, altree
-
convert, altree
-
add
-
s

o

reference: Bardel, Danjean, Hugot, Darlu, Gen
in (2005), "On the use of haplotype phylogeny to
detect disease susceptibility loci", BMC Genetics, 6:24.



AMELIA

o

full name: Allele Matching Empirical Locus
-
specific Integrated Association test

o

version:

o

description: AMELIA is a program that employs allele
matching to analyse the effects of rare variants
within a specific locus. There is increasing evidence that rare variants play a role in some complex
traits, but their analysis is not straightforward. Locus
-
based tests become necessary due to low
power in
rare variant single
-
point association analyses. In addition, variant quality scores are
available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has
been developed as an allele
-
matching approach that is robust to th
e presence of both directions of
effect for variants within the locus analysed.

o

authors: Eleftheria Zeggini's group (Wellcome Trust Sanger Institute)

o

web/ftp: http://www.sanger.ac.uk/resources/software/amelia/

o

source code language: R

o

operating systems: UNI
X, Linux

o

executables:

o

reference:



ANALYZE

o

full name:

o

version: 2.1 (feb 14, 1996)

o

description: a set of useful accessory programs to the LINKAGE package. it simplifies the
performance of a large array of parametric and nonparametric tests for linkage and ass
ociation on
data entered in LINKAGE format pedigree and parameter files.

o

authors: Joseph

Terwilliger

o

web/ftp: http://www.helsinki.fi/~tsjuntun/linkage/analyze/
;
http://linkage.cpmc.columbia.edu/index_files/Page434.htm
;

o

ftp://ftp.ebi.ac.uk/pub/software/lin
kage_and_mapping/linkage_cpmc_columbia/analyze/

o

source code language: Pascal

o

operating systems: UNIX (SunOS/Solaris/OSF1..)

o

executables: analysis (script), analyzeprep, downfreq, extract, (homog), homogpos, homogpre,
hrrlamb, hrrlambprep, hrrmult, hrrprep,

interpretation, locusorder, pedprepare, polylocus, sib2link,
sibpairna, sibprepna, tdtlikena

o

reference:



ANCESTRY

o

full name:

o

version:

o

description: This application aims at providing the user with an easy to use web
-
based user interface
to compute individua
l ancestry estimates using the Maximum Likelihood Estimation method. This
website also allows registered users to manage genotype and marker/allele frequency files.
Registration is optional.

o

authors: Van
-
Anh Tran (email: vananh.tran@case.edu), Thomas Dyer,

Guo
-
Qiang Zhang, Jill
Barnholtz
-
Sloan (email: jsb42@case.edu)

o

web/ftp: http://ciil.case.edu:3000

o

source code language: Ruby on Rails, FORTRAN

o

operating systems: web
-
based

o

executables:

o

reference: Hanis, Chakraborty, Ferrell, Schull (1986), "Individual
admixture estimates: disease
associations and individual risk of diabetes and gallbladder disease among Mexican
-
Americans in
Starr County, Texas", American Journal of Physical Anthropology, 70(4):433
-
441.



ANCESTRYMAP

o

full name:

o

version: 2.0

o

description: AN
CESTRYMAP screens through the genome in a recently mixed population such as
African Americans, searching for segments with increased ancestry from one of the ancestral
populations, which can indicate the position of disease genes

o

authors: Arti Tandon (emai
l: atandon@broad.mit.edu), Nick Patterson (email: nickp@broad.mit.edu),
David Reich.

o

web/ftp: http://genepath.med.harvard.edu/~reich/Software.htm

o

source code language:

o

operating systems: UNIX, Linux

o

executables:

o

reference: Patterson, Hattangadi, Lane, Lohm
ueller, Hafler, Oksenberg, Hauser, Smith, O'Brien,
Altshuler, Daly, Reich (2004), "Methods for high
-
density admixture mapping of disease genes",
American Journal of Human Genetics, 74(5):97
-
1000



ANNOVAR

o

full name: functional ANNOtation of genetic VARiants

o

version: Feb 2010

o

description: ANNOVAR is an efficient software tool to utilize update
-
to
-
date information to
functionally annotate genetic variants detected from diverse genomes (including human genome
hg18, hg19, as well as mouse, worm, fly, yeast and ma
ny others). Given a list of variants with
chromosome, start position, end position, reference nucleotide and observed nucleotides,
ANNOVAR can perform: 1. gene
-
based annotation. 2. region
-
based annotation. 3. filter
-
based
annotation. 4. other functionaliti
es.

o

authors: Kai Wang (Univ Pennsylvania)

o

web/ftp: http://www.openbioinformatics.org/annovar/

o

source code language:

o

operating systems:

o

executables:

o

reference: Wang, Li, Hakonarson (2010), "ANNOVAR: Functional annotation of genetic variants from
next
-
genera
tion sequencing data", Nucleic Acids Research, 38:e164.



ANTMAP

o

full name:

o

version: 1.2 (June 2006)

o

description: Ordering markers when the number of loci is large is a special case of the traveling
salesman problem. ANTMAP is a system based on the Ant
Colony Optimization to solve this problem.
ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage
map rapidly.

o

authors: Hiroyoshi Iwata (email: iwata@lbm.ab.a.u
-
tokyo.ac.jp)

o

web/ftp: http://lbm.ab.a.u
-
tokyo.ac.jp/~i
wata/antmap/

o

source code language: Java

o

operating systems: MS
-
Windows, MacOS, Linux, UNIX(Solaris)

o

executables:

o

reference: Iwata, Ninomiya (2006) "AntMap: constructing genetic linkage maps using an ant colony
optimization algorithm", Breeding Science, 56:3
71
-
377.

o

[PDF]



APE

o

full name: Allelic Path Explorer

o

version: 1.0

o

description: Extends partially observed genotype data to the whole pedigree. Can be used for
generating starting points for MCMC samplers and for checking that the genotype data are
consistent

with the pedigree structure.

o

authors: Matti Pirinen, Dario Gasbarra (University of Helsinki, Finland)

o

web/ftp: http://www.helsinki.fi/~mpirinen/download

o

source code language: C

o

operating systems: UNIX

o

executables:

o

reference: Pirinen, Gasbarra (2006), "Fin
ding consistent gene transmission patterns on large and
complex pedigrees", IEEE/ACM cransactions on Computational Biology and Bioinformatics, 3(3):252
-
262



APL
-
OSA

o

full name: Association in the Presence of Linkage with Ordered Subset Analysis

o

version:

o

desc
ription: In the presence of genetic heterogeneity, APL
-
OSA can identify a genetically
homogenous subset of families based on a trait
-
related covariate. APL
-
OSA then tests the
relationship between the association statistics (i.e., the APL statistics) calcul
ated based on the subset
and the family
-
specific covariate. APL
-
OSA is based on the OSA method for linkage and the family
-
based association test, APL. Thus, APL
-
OSA has similar properties with OSA and APL. Bi
-
alleleic
markers such as SNPs are accepted by A
PL
-
OSA. APL
-
OSA is a single
-
marker test and considers one
covariate each time.

o

authors: Elizabeth R. Hauser, email: apl
-
osa@chg.duhs.duke.edu

o

web/ftp: http://wwwchg.duhs.duke.edu/research/aplosa.html

o

source code language: C++

o

operating systems: UNIX(Solari
s), Linux(RedHat), MS
-
Windows(XP)

o

executables:

o

reference: Martin, Bass, Hauser, Kaplan (2003), "Accounting for linkage in family
-
based tests of
association with missing parental genotypes", American Journal of Human Genetics, 73:1016
-
1026

o

Hauser, Watanabe,

Duren, Bass, Langefeld, Boehnke (2004), "Ordered subset analysis in genetic
linkage mapping of complex traits", Genetic Epidemiology, 27:53
-
63.

o

Chung, Hauser, martin (2006), "The APL test: extension to general nuclear families and haplotypes
and examinati
on of its robustness", Human Heredity, 61:189
-
199.



APM

o

full name: Affected Pedigree
-
Member Method

o

version: July 1993

o

description:

o

authors: Daniel E. Weeks (University of Oxford and University of Pittsburgh, email:
dweeks@watson.hgen.pitt.edu), Mark Schroed
er (email: mark@holmes.hgen.pitt.edu)

o

web/ftp: http://watson.hgen.pitt.edu/register/soft_doc.html registration page at:
http://watson.hgen.pitt.edu/register

o

source code language: C and Pascal and FORTRAN

o

operating systems: UNIX, VMS, MS
-
DOS

o

executables: ap
m, sim, apmmult, simmult, chapm, hist

o

reference: Weeks and Lange, American Journal of Human Genetics, 42(2):315
-
326 (1988). [
abstract
]



ARIEL

o

full name: Accumulation of Rare v
ariants Integrated and Extended Locus
-
specific test

o

version:

o

description: ARIEL explores the effects of rare variants within complex traits through locus
-
based
analysis. There is increasing evidence that rare variants play a role in some complex traits, bu
t their
analysis is not straightforward. Locus
-
based tests become necessary due to low power in rare variant
single
-
point association analyses. In addition, variant quality scores are available for sequencing data,
but are rarely taken into account. To ena
ble this analysis, ARIEL has been developed as a locus
-
wide
regression
-
based collapsing approach that incorporates variant quality scores.

o

authors: Eleftheria Zeggini's group (Wellcome Trust Sanger Institute)

o

web/ftp: http://www.sanger.ac.uk/resources/soft
ware/ariel/

o

source code language: R

o

operating systems: UNIX, Linux

o

executables:

o

reference:



ARLEQUIN

o

full name: (French translation of "Arlecchino", a character of the Italian "Commedia dell'Arte". He
has many aspects, but can switch among them very easily
according to needs and necessities.
Similarly, this software is about the study of genetic polymorphism.)

o

version: 3.1 (September 2006)

o

description: an exploratory population genetics software environment able to handle large samples
of molecular data
(RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing
conventional genetic data (standard multi
-
locus data or mere allele frequency data).

o

authors: Laurent Excoffier (email: laurent.excoffier@zoo.unibe.ch), Guillaume Laval, Ste
fan
Schneider (University of Berne, Switzerland)

o

web/ftp: http://cmpg.unibe.ch/software/arlequin3/

o

http://lgb.unige.ch/arlequin/

o

source code language:

o

operating systems: MS
-
Windows (95/98/NT/2000/XP)

o

executables:

o

reference: Excoffier, Laval, Schneider (200
5), "Arlequin ver. 3.0: an integrated software package for
population genetics data analysis", Evolutionary Bioinformatics Online, 1:47
-
50.

o

Schneider, Kueffer, Roessli, Excofier, "Arlequin: A software for population genetic data analysis. Ver
1.1", (Geneti
cs and Biometry Lab, Dept. of Anthropology, University of Geneva, 1997);

o

User's manual (PDF, v1.1)

o

User's manual (PDF, v3.1)



ARP.GEE

o

full name:

o

version: 0.1.0 (April 2005)

o

description: Simultaneously estimate a trait
-
locus position and its genetic effects
for affected
relative pairs (ARP) by one of two methods. Either allow a different trait
-
locus effect for each ARP
type, or constrain the trait
-
locus effects according to the marginal effect of a single susceptibility
locus. We include a goodness of fit sta
tistic for the constrained model.

o

authors: Daniel Schaid, Jason Sinnwell (Mayo Clinic)

o

web/ftp: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

o

source code language: R/S
-
PLUS

o

operating systems:

o

executables:

o

reference:



ASP/ASPSHARE

o

full n
ame:

o

version: 1.2 (June 2002) (Warning: the earlier version contains a bug)

o

description: ASP a power calculator for gene mapping using a sibpair design (concordant or
discordant). ASPSHARE complements ASP in that it allows rapid calculation of the expected

ibd
sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the
respective parameters.

o

authors: Michael Krawczak

o

web/ftp: http://www.uni
-
kiel.de/medinfo/mitarbeiter/krawczak/download/

o

source code language:

o

operating

systems:

o

executables:

o

reference: online manual for ASP



ASPEX

o

full name: Affected Sib Pairs EXclusion map

o

version: 2.5 (September 2003)

o

description: a set of programs for performing multipoint exclusion mapping of affected sibling pair
data for discrete tr
aits.

o

authors: David Hinds (email: dahinds@users.sourceforge.net) Neil Risch (Stanford Univ),

o

web/ftp: http://aspex.sourceforge.net/

o

previously: ftp://lahmed.stanford.edu/pub/aspex

o

source code language: C, Tcl, Perl (the graphic script requires xmgr, avail
able from
ftp://ftp.teleport.com/pub/users/pturner/acegr
)

o

operating systems: UNIX (Solaris/SunOS/IRIX/OSF
-
1), Linux

o

executables: sib_ibd, sib_tdt, sib_phase, sib_map, sib_kin, sib_clean

o

reference: online manual

(PDF)



ASSOCIATIONVIEWER

o

full name:

o

version:

o

d
escription: AssociationViewer is a Java application used to display SNPs in a genetic context.
Supplementary data (such as genes or LD plots) is downloaded from various public data sources on
the fly and saved locally in a cache. Custom data can be added a
s supplementary tracks.

o

authors:

o

web/ftp: http://associationviewer.vital
-
it.ch/

o

source code language: Java

o

operating systems:

o

executables:

o

reference: Martin, Valsesia, Telenti, Xenarios, Stevenson (2009), "AssociationViewer: a scalable and
integrated softw
are tool for visualization of large
-
scale variation data in genomic context",
Bioinformatics, 25(5):662
-
663.



AUTOSCAN

o

full name:

o

version: 1.0.1 (February 2000)

o

description: a helper program to automate the tedious process of the creation of input files
from
genotype data of genome
-
wide scans

o

authors: T Hiekkalinna, L Peltonen (UCLA)

o

web/ftp: http://www.helsinki.fi/~tsjuntun/autoscan/

o

source code language: C and UNIX
-
shell (Bourne)

o

operating systems: UNIX (Solaris/DEC
-
UNIX)

o

executables: autostart, autosca
n10.sh

o

reference: American Journal of Human Genetics, supp, 65 . (
abstract
) (1999)



BAMA

o

full name: Bayesian Analysis of Multilocus Association

o

version:

o

description: This is a program to

select a trait
-
associated subset of markers among many candidates.
The program is based on Bayesian modeling/estimation and it suits for both quantitative and
qualitative traits. It can handle bi
-

and multiallelic markers as well as applied in situations
where part
of the marker genotypes may be missing. As an output of the program, one obtains posterior
estimate of number and positions of trait
-
associated markers.

o

authors: Mikko J Sillanpaa, Riika Kilpikari

o

web/ftp: http://www.rni.helsinki.fi/~mjs/

o

source

code language: C

o

operating systems: Linux

o

executables:

o

reference: R Kilpikari, MJ Sillanpaa (2003), "Bayesian analysis of multilocus association in
quantitative and qualitative traits", Genetic Epidemiology, 25:122
-
135.



BARS

o

full name: Bayesian Adaptive R
egression Splines

o

version:

o

description: The BARS tests is a statistical method that bridges the gap between single
-
locus and
haplotype
-
based tests of association. It is based on the non
-
parametric regression techniques
embodied by Bayesian Adaptive Regress
ion Splines.

o

authors: Garrick Wallstrom, RE Kass

o

web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

o

source code language: R

o

operating systems: Linux

o

executables:

o

reference: Zhang, Roeder, Wallstrom, Devlin (2003), "Integration of associative
statistics over
genomic regions using Bayesian Adaptive Regression Splines", Human Genomics, 1:20
-
29.



BAYESFST

o

full name:

o

version:

o

description: Bayesian estimation of the coancestry coefficient FST

o

authors: DJ Balding (email: d.balding@ic.ac.uk), KL Ayres,

MA Beaumont, P O'Reilly

o

web/ftp: http://www.reading.ac.uk/Statistics/genetics/software.html

o

source code language: C

o

operating systems:

o

executables:

o

reference: Balding (2003), "Likelihood
-
based inference for genetic correlation coefficients",
Theoretical P
opulation Biology, 63:221
-
230

o

Beaumont, Balding (2004), "Identifying adaptive genetic divergence among populations from
genome scans", Molecular Ecology, 13:969
-
980.



BDGEN

o

full name:

o

version: 1.7

o

description: a powerful database software with improvement t
ools for paternity testing, database
searching (like CODIS) and NRC II recommendations based formulae for investigating likelyhood
ratios in putative contributors to crime evidences. Additional genetic population parameters
estimations are added in this ve
rsion. Only spanish version available.

o

authors: Martinez Gustavo (email:ggmartinez@arnet.com.ar), Vazquez Sebastian, and Vicentin Ariel
(email: bdgen@yahoo.com.ar)

o

web/ftp: http://www.simedic.com.ar/bdgen.htm

o

source code language:

o

operating systems: MS
-
Win
dows

o

executables:

o

reference: V Vazquez, A Vicentin, L Vazquez, and G Martinez (2002) "Nuevo programa BDGen, como
base de datos y herramienta de analisis estadistico de patrones geneticos". VII meeting of the
Spanish
-
Portuguese Group for the International S
ociety for Forensic Genertics. Barcelona, June 2002.



BEAGLE

o

full name:

o

version: 3.2.1 (May 2010)

o

description: BEAGLE is a state of the art software package for analysis of large
-
scale genetic data sets
with hundreds of thousands of markers genotyped on tho
usands of samples. BEAGLE can

o

phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent
-
offspring pairs, and
parent
-
offspring trios.

o

infer sporadic missing genotype data.

o

impute ungenotyped markers that have been genotyped in a
reference panel.

o

perform single marker and haplotypic association analysis.

o

detect genetic regions that are homozygous
-
by
-
descent in an individual or identical
-
by
-
descent in
pairs of individuals.

o

authors: Brian L Browning, Sharon R Browning (email: brownin
g@stat.auckland.ac.nz),

o

web/ftp: http://www.stat.auckland.ac.nz/~browning/beagle/beagle.html

o

source code language: Java

o

operating systems: MS
-
Windows, Linux, UNIX(Solaris), MacOS

o

executables:

o

reference: Browning SR and Browning BR (2007), "Rapid and accura
te haplotype phasing and
missing
-
data inference for whole
-
genome association studies by use of localized haplotype
clustering", American Journal of Human Genetics, 81(5):1084
-
1097

o

Browning BR and Browning SR (2007), "Efficient multilocus association testin
g for whole genome
association studies using localized haplotype clustering", Genetic Epidemiology, 31:365
-
375.



BEAGLECALL

o

full name:

o

version: 1.0.0 (September 2010)

o

description: BEAGLECALL is a software package for simultaneous genotype calling and haplot
ype
phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and
output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses
both allele signal intensity data and inter
-
marker corre
lation to call genotypes. BEAGLECALL is
designed for use with high
-
density SNP arrays, and it uses the BEAGLE haplotype frequency model to
model inter
-
marker correlation.

o

authors:

o

web/ftp: http://faculty.washington.edu/browning/beaglecall/beaglecall.html

o

s
ource code language: Java

o

operating systems: MS
-
Windows, UNIX, Linux, MacOS

o

executables:

o

reference: Browning, Yu (2009), "Simultaneous genotype calling and haplotype phase inference
improves genotype accuracy and reduces false positive associations for gen
ome
-
wide association
studies", American Journal of Human Genetics, 85:847
-
861.



BEAM

o

full name: Bayesian Epistasis Association Mapping

o

version:

o

description: BEAM treats the disease
-
associated markers and their interactions via a bayesian
partitioning model
and computes, via Markov chain Monte Carlo, the posterior probability that each
marker set is associated with the disease.

o

authors: Yu Zhang, Jun S Liu (Harvard University)

o

web/ftp: http://www.people.fas.harvard.edu/~junliu/BEAM/

o

source code language: C++

o

operating systems: UNIX, Linux, DOS

o

executables:

o

reference: Zhang, Liu (2007), "Bayesian inference of epistatic interactions in case
-
control studies",
Nature, 39:1167
-
1173.



BETA

o

full name:

o

version: Jan 1998

o

description: non
-
parametric linkage analysis usin
g allele sharing in sib pairs

o

authors: A Collins (email: arc@soton.ac.uk), NE Morton (University of Southampton, UK)

o

web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/BETA

o

source code language: C

o

operating systems: UNIX(SUN..)

o

executables: beta

o

refer
ence: Morton (1996), Procee
dings of the National Academy of Sciences , 93:3471
-
3476
; Collins,
Morton (1996), Procee
dings of the National Academy of Sciences , 93:9177
-
9181; Lio, Morton (1997),
Procee
dings of the National Academy of Sciences , 94:5344
-
5348;

online manual



BIMBAM

o

full name: Bayesian IMputation
-
Based Association Mapping

o

version: 0.95

o

description:

o

authors: B Servin, M Stephens

o

web/ftp: http://stephenslab.uchicago.edu/software.html

o

source code language:

o

operating systems:

o

executables:

o

reference:
Servin, Stephens (2007), "Imputation
-
based analysis of association studies: candidate
genes and quantitative traits", PLoS Genetics, 3(7):e114.
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030114



BIOIDE

o

full name: BIOmedical Integrate
d Discovery Environment

o

version:

o

description: Developed by scientists for scientists, our Biomedical Integrated Discovery Environment
provides easy access to a rapidly expanding collection of data analysis tools and interrelated
biomedical information in a single easy
-
to
-
use software pack
age with an extremely high benefit/cost
ratio. Our component
-
based software/data integration platform can quickly transform fragmented
enterprise legacy data and software into an integrated suite of tools and knowledge base to achieve
maximal usability, in
teroperability, scalability, and extensibility.

o

authors:

o

web/ftp: http://www.htbiology.com/software.php

o

source code language:

o

operating systems:

o

executables:

o

reference:



BIOLAD
-
DB

o

full name:

o

version: 3.0.1

o

description: The BiolAD
-
DB system is a research bio
informatics system for inputting, validating,
organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database
schema employs design principles for handling complex clinical information, such as response items
in genetic
questionnaires. Data access and validation is provided by the BiolAD
-
DB client application,
which features a data validation engine tightly coupled to a graphical user interface. Data integrity is
provided by the password protected BiolAD
-
DB SQL compliant
server database. BiolAD
-
DB tools
further provide functionalities for generating customized reports and views.

o

authors: David Nielsen (email: nielsen@rockefeller.edu), Marty Leidner (email:
marty@rockefeller.edu), Chad Haynes (email: haynesc@rockefeller.edu
), Michael Krauthammer
(email: michael.krauthammer@yale.edu), Mary Jeanne Kreek (email: kreek@rockefeller.edu)

o

web/ftp: http://www.rockefeller.edu/biolad
-
db/

o

source code language: Python

o

operating systems: MS
-
Windows

o

executables:

o

reference: Nielsen, Leidne
r, Haynes, Krauthammer, Kreek (2007), "The BiolAD
-
DB system
-

an
informatics system for clinical and genetic data", Molecular Diagnosis & Therapy, 11(1):15
-
19.



BIRDSUITE

o

full name:

o

version:

o

description: The Birdsuite is a fully open
-
source set of tools to
detect and report SNP genotypes,
common Copy
-
Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples
processed with the Affymetrix platform. While most of the components of the suite can be run
individually (for instance, to only do SNP ge
notyping), the Birdsuite is especially intended for
integrated analysis of SNPs and CNVs.

o

authors: Joshua Korn et al. (Broad Institute)

o

web/ftp: http://www.broadinstitute.org/scientific
-
community/science/programs/medical
-
and
-
population
-
genetics/birdsuite/b
irdsuite

o

source code language:

o

operating systems:

o

executables:

o

reference: Korn, Kuruvilla, McCarroll, Wysoker, Nemesh, Cawley, Hubbell, Veitch, Collins, Darvishi,
Lee, Nizzari, Gabriel, Purcell, Daly, Altshuler (2008), "Integrated genotype calling and
association
analysis of SNPs, common copy number polymorphisms and rare CNVs", Nature Genetics, 40:1253
-
1260.



BLADE

o

full name: Bayesian LinkAge DisEquilibrium mapping

o

version: v2

o

description:

o

authors: Jun Liu (Harvard Univ) (email: jliu@stat.harvard.edu)

o

w
eb/ftp: http://www.people.fas.harvard.edu/~junliu/index1.html

o

http://www.fas.harvard.edu/~junliu/TechRept/03folder/bladev2.tgz

o

source code language:

o

operating systems:

o

executables:

o

reference: Liu, Sabatti, Teng, Keats, Risch (2001), "Bayesian analysis of h
aplotypes for linkage
disequilibrium mapping", Genome Research, 11:1716
-
1724.

o

Lu, Niu, Liu (2003), "Haplotype information and linkage disequilibrium mapping for single nucleotide
polymorphisms", Genome Research, 13:2112
-
2117.



BLOCK

o

full name: Blocking Gibb
s sampler for pedigree analysis

o

version: 2.0.0 (Dec 1996)

o

description: the programs allow you to perform general pedigree analysis on a general pedigree with
any number of loops. It also allows you to perform two
-
point linkage analysis on a general pedigre
e
with an arbitrary number of alleles.

o

authors: Claus Skaanning Jensen (email: claus@cs.auc.dk) (Aalborg University, Denmark)

o

web/ftp: http://www.cs.auc.dk/~claus/block.html

o

or a copy from http://hpcio.cit.nih.gov/lserver/BLOCK.html

o

ftp://ftp.cs.auc.dk/pub
/packages/block/current

o

source code language:

o

operating systems: MS
-
DOS, Linux, UNIX(Solaris, Irix 64, AIX 3.2.5, DEC alpha)

o

executables: block, theta

o

reference: Jensen, Kong and Kjaerulff, "Blocking
-
Gibbs Sampling in Very Large Probabilistic Expert
System
s", International Journal of Human
-
Computer Studies, 647
-
666 (1995).



BMAPBUILDER

o

full name:

o

version: 2.1(beta)

o

description:

o

authors:

o

web/ftp: http://bios.ugr.es/BMapBuilder/

o

source code language: Java

o

operating systems: MS
-
Windows, MacOS, UNIX, Linux

o

executables:

o

reference: Abad
-
Grau, Montes, Sebastiani (2006), "Building chromosome
-
wide LD maps",
Bioinformatics, 22(16):1933
-
1934.



BOOLD

o

full name:

o

version: 1.1 (July 2002)

o

description: a set of programs for calculations under different linkage disequilib
rium (LD) distribution
models

o

authors: YS Aulchenko (email: aulchenko@epib.fgg.eur.nl) (Erasmus University Medical School. The
Netherlands)

o

web/ftp: http://www.geneticepi.com/Research/software/software.html

o

http://www.geneticepi.com/Research/software/booLD
-
1.1.tar.gz

o

source code language: C++, FORTRAN 77, Perl

o

operating systems: UNIX, Linux

o

executables: kLD, lsqLD, booit.pl

o

reference:



BOOST

o

full name: BOolean Operation based Screening and Testing

o

version:

o

description:

o

authors: Xiang Wan, Can Yang (email: ee
yang@ust.hk), Qiang Yang, Hong Xue, Xiaodan Fan, Nelson
Tang, Weichuan Yu

o

web/ftp: http://bioinformatics.ust.hk/BOOST.html

o

source code language:

o

operating systems:

o

executables:

o

reference: Wan, Yang, Yang, Xue, Fan, Tang, Yu (2010), "BOOST: a Boolean
representation
-
based
method for detecting SNP
-
SNP interactions in genome
-
wide association studies"", American Journal
of Human Genetics, 87:325
-
340.



BOOSTRAPPER

o

full name:

o

version: 1.0

o

description: Robust haploblock border reliability estimation tool is im
plemented for LD based
haploblock detection method. The most important new features are bootstrapping and overlapping
block borders.

o

authors:

o

web/ftp: http://bioinfo.ebc.ee/download/

o

source code language:

o

operating systems: MS
-
Window, Linux

o

executables:

o

re
ference:



BOREL (see also PANGAEA)

o

full name:

o

version: July 1996

o

description: Programs for inference of genealogical relationships from genetic data, including sibship
inference.

o

authors: Elizabeth A Thompson (University of Washington), Ian Painter (now at
NCSU, email:
ian@statgen.ncsu.edu)

o

web/ftp: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml

o

ftp://ftp.u.washington.edu/pub/user
-
supported/pangaea/PANGAEA/BOREL

o

source code language: C

o

operating systems: UNIX(DEC
-
UNIX/..)

o

executables:

o

reference
:



BOTTLENECK

o

full name:

o

version: 1.2.02

o

description: a program for detecting recent effective population size reductions from allele data
frequencies

o

authors: Sylvian Piry

o

web/ftp: http://www.montpellier.inra.fr/URLB/bottleneck/bottleneck.html

o

source code
language:

o

operating systems: MS
-
Windows (95)

o

executables:

o

reference: Piry, Luikart, Cornuet (1999), "BOTTLENECK: a computer program for detecting recent
reductions in the effective size using allele frequency data", Journal of Heredity, 90:502
-
503.



BPPH

o

fu
ll name: Berkeley method for Perfect Phylogeney Haplotyping

o

version: April 2003

o

description: a program for inferring haplotypes from genotypes to determine if there are resulting
haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In

population genetic terms,
BPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could
have evolved on a coalescent under the no
-
recombination, infinite sites model.

o

authors: Ren
-
Hua Chuang, Dan Gusfield (UC Davis) (email:

gusfield@cs.ucdavis.edu)

o

web/ftp: http://wwwcsif.cs.ucdavis.edu/~gusfield/bpph.html

o

source code language:

o

operating systems:

o

executables:

o

reference: D. Gusfield (2002), "Haplotyping as perfect phylogeny: conceptual framework and
efficient solutions", In P
roceedings of RECOMB, Sixth Annual Conference on Research in
Computational Molecular Biology, pp.?
-
?.



BQTL

o

full name: Bayesian Quantitative Trait Locus mapping

o

version:

o

description: for the mapping of genetic traits from line crosses and recombinant inbred

lines. It
performs (1) maximum likelihood estimation of multi
-
gene models; (2) Bayesian estimation of multi
-
gene models via Laplace Approximations; and (3) interval mapping and composite interval mapping
of genetic loci

o

authors: Justin Borevitz, Charles C
. Berry (UCSD)

o

web/ftp: http://hacuna.ucsd.edu/bqtl/

o

source code language: S, C, FORTRAN. The software is engineered to work in conjunction with R.

o

operating systems: UNIX, MS
-
Windows, MacOS

o

executables: cvl.blup.R(), cvl.epi.R(), cvl.jack.R(), cvl.qtl.eff
ect.R(), read.map.R(), read.markers.R().

o

reference: JO Borevitz, JN Maloof, J Lutes, T Dabi, JL Redfern, GT Trainer, JD Werner, T Asami, CC
Berry, D Weigel, J Chory (2002), "Quantitative trait loci controlling light and hormone response in
two accessions o
f Arabidopsis thaliana", Genetics, 160(2):683
-
696.



BREAKDANCER

o

full name:

o

version:

o

description: BreakDancer provides genome
-
wide detection of structural variants from next
generation paired
-
end sequencing reads. BreakDancerMax predicts five types of
structural variants:
insertions, deletions, inversions, inter
-

and intra
-
chromosomal translocations from next
-
generation
short paired
-
end sequencing reads using read pairs that are mapped with unexpected separation
distances or orientation.

o

authors:

o

web/ft
p: http://gmt.genome.wustl.edu/breakdancer/current/

o

source code language: Perl, C++

o

operating systems:

o

executables:

o

reference: Chen, Wallis, McLellan, Larson, Kalicki, Pohl, McGrath, Wendl, Zhang, Locke, Shi, Fulton,
Ley, Wilson, Ding, Mardis (2009), "Brea
kDancer: an algorithm for high
-
resolution mapping of
genomic structural variation", Nature Methods, 6:677
-
681.



CAROL

o

full name: Combined Annotation scoRing toOL

o

version:

o

description: CAROL is a combined functional annotation score of non
-
synonymous coding
variants. A
major challenge in interpreting whole
-
exome data is predicting which of the discovered variants are
deleterious or neutral. To address this question in silico, we have developed a score called Combined
Annotation scoRing toOL (CAROL),which comb
ines information from two bioinformatics tools:
PolyPhen
-
2 and SIFT, in order to improve the prediction of the effect of non
-
synonymous coding
variants. The combination of annotation tools can help improve automated prediction of whole
-
genome/exome non
-
syn
onymous variant functional consequences.

o

authors: Eleftheria Zeggini's group (Wellcome Trust Sanger Institute)

o

web/ftp: http://www.sanger.ac.uk/resources/software/carol/

o

source code language: R

o

operating systems:

o

executables:

o

reference:



CARTHAGENE

o

full nam
e:

o

version: 1.0 (January 2006)

o

description: It is a genetic/radiation hybrid mapping software. CARTHAGENE looks for multiple
populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood
estimation and powerful ordering alg
orithms inspired from TSP (Traveling Salesman Problem)
technology. It can handle large data sets made up of different populations (either F2 backcross,
recombinant inbred lines, F2 intercross, phase known outbreds, haploid/diploid radiation hybrids). It
ca
n also exploit existing syntenic relationships between the organism mapped and a reference
(sequenced) organism for accurate dense RH mapping.

o

authors: P Chabrier, D de Givry, T Faraut, C Gaspin, T Schiex (INRA, Toulouse, France)

o

web/ftp: http://www.inra.f
r/mia/T/CarthaGene/

o

source code language: C++,Tcl/Tk

o

operating systems: MS
-
Windows, UNIX(Solaris), Linux. Sources are available for other operating
systems (GPL/QPL).

o

executables:

o

reference: Schiex,Gaspin, Proceedings of the International Conference on
Intelligent Systems for
Molecular Biology (ISMB) (1997).

o

Givry, Bouchez, Chabrier, Milan, Schiex (2005), "CARTHAGENE: multipopulation integrated genetic
and radiation hybrid mapping", Bioinformatics, 21(8):1703
-
1704.



CASAVA

o

full name: Consensus Assessment
of Sequence And VAriation

o

version: v1.6

o

description: Illumina's CASAVA software captures summary information for resequencing and
counting studies and places the data in a compact structure for visualization within GenomeStudio
Software or publicly availab
le analysis tools. CASAVA can create genomic builds, call SNPs, detects
indels, and count reads from data generated from one or more runs of the Genome Analyzer across
a broad range of sequencing applications.

o

v.1.6 highlights: 1. complete secondary analys
is software package, including facilities for alignment,
reference
-
guided assembly, SNP/indel calling and counting for RNA applications. 2. new methods for
gapped, multiseed alignments that reduce artifactual mismatches. 3. new indel detection method,
and
improved SNP calling on longer Genome Analyzer reads.

o

authors: (Illumina)

o

web/ftp: http://www.illumina.com/software/genome_analyzer_software.ilmn

o

source code language:

o

operating systems:

o

executables:

o

reference:

o

price:



CASPAR

o

full name: Computerized Affecte
d Sibling Pair Analyzer and Reporter

o

version:

o

description: CASPAR's main novel feature is conditional linkage analyses, in which the population can
be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses
simulat
ion to overcome the problems inherent in such multiple testing.

o

authors: Richa Agarwala (email: richa@helix.nih.gov
)

and Alejandro Schaffer (email:
schaffer@helix.nih.gov); other participants include Jeremy Buhler, Kenneth Gabbay, Marek Kimmel,
David Owerb
ach

o

web/ftp: http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

o

ftp://fastlink.nih.gov/pub/caspar

o

source code language: C

o

operating systems: UNIX

o

executables:

o

reference: Am Soc Hum Genet annual meeting 1995 (Buhler, et. al. American Journal of Hu
man
Genetics, 57 Supp, A171 (1995));

o

Buhler, et. al. (1997) Human Heredity, 47(4):211
-
222.



CATS

o

full name: power Calculator for Association with Two Stage design

o

version: 0.0.1

o

description: CATS calculates the power and other useful quantities for
two
-
stage genome
-
wide
association studies

o

authors: Andrew Skol (email: askol@umich.edu)

o

web/ftp: http://www.sph.umich.edu/csg/abecasis/CaTS/

o

source code language: C++

o

operating systems: UNIX, Linux, MS
-
Windows, MacOS

o

executables: cats (graphical interface
for MS
-
Windows, MacOS, and Linux), cats
-
test (Linux
command line)

o

reference: Skol, Scott, Abecasis, Boehnke (2006), "Joint analysis is more efficient than replication
-
based analysis for two
-
stage genome
-
wide association studies", Nature Genetics, 38:209
-
21
3.



CC
-
QLS

o

full name: Case
-
Control Quasi
-
Likelihood Score test

o

version: 1.3 (March 2006)

o

description:

o

authors: Catherine Bourgain, Sabine Hoffjan, Raluca Nicolae, Dina Newman, Lori Steiner, Karen
Walker, Rebecca Reynolds, Carole Ober, Mary Sara McPeek

o

web/f
tp: http://www.stat.uchicago.edu/~mcpeek/software/CCQLSpackage1.3/

o

source code language:

o

operating systems: UNIX

o

executables:

o

reference: Bourgain, Hoffjan, Nicolae, Newman, Steiner, Walker, Reynolds, Ober, McPeek (2003),
"Novel case
-
control test in a found
er population identifies p
-
selectin as an Atopy
-
susceptibility
locus", American Journal of Human Genetics, 73(3):612
-
626



CCRAVAT (see also QUTIE
)

o

full name: Case
-
Control RAre Variant Analysis Tool

o

version:

o

description: Enabling the analysis of rare variant
s in large
-
scale case control and quantitative trait
association studies. CCRaVAT (Case
-
Control Rare Variant Analysis Tool) and QuTie (Quantitative Trait)
are software packages that enable efficient large
-
scale analysis of rare variants across specific
reg
ions or genome
-
wide. These programs implement a rare variant super
-
locus or collapsing method
that investigates the accumulation of rare variant alleles in either a case
-
control or quantitative trait
study design.

o

authors: Eleftheria Zeggini's group (Wellc
ome Trust Sanger Institute)

o

web/ftp: http://www.sanger.ac.uk/resources/software/rarevariant/

o

source code language:

o

operating systems:

o

executables:

o

reference:



CCREL

o

full name: Case
-
Control association analysis with RELlated individuals

o

version: 0.3
(December 2005)

o

description: CCREL is a program for case
-
control genetic analysis that takes relatedness between
individuals into account. It will perform single
-
marker and haplotypic tests, however it will only work
with SNP or other biallelic markers.

o

au
thors: Sharon R. Browning (e
-
mail: browning@stat.auckland.ac.nz)

o

web/ftp: http://www.stat.auckland.ac.nz/~browning/ccrel/ccrel.htm

o

source code language: R with Perl and C

o

operating systems: Unix/Linux

o

executables:

o

reference: Browning, Briley, Briley, Chand
ra, Charnecki, Ehm, Johansson, Jones, Karter, Yarnall,
Wagner (2005), "Case
-
control single marker and haplotypic association analysis of pedigree data",
Genetic Epidemiology, 28:110
-
122.



CEPH2CRI

o

full name:

o

version: May 1994

o

description: convert output fro
m CEPH DBMS to CRIMAP format

o

authors: John Attwood (Sanger Centre, UK) ( email: ja1@sanger.ac.uk)

o

web/ftp: http://www.gene.ucl.ac.uk/public
-
files/packages/linkage_utils/ceph2cri/

o

source code language: Pascal

o

operating systems: MS
-
DOS

o

executables:

o

reference
:



CEPH2MAP

o

full name:

o

version:

o

description: it is developed from crimap v2.4 for use with the map suite of programs.

o

authors:

o

web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ceph2map

o

source code language: C

o

operating systems:

o

executables: ceph2map

o

reference:



CFC

o

full name: Contribution, Inbreeding (F) and Coancestry

o

version: 1.0 (April 2006)

o

description: This is a general
-
purpose program for monitoring genetic diversity. CFC allows for
several pedigree analyses such as: (1) computing inbreeding coef
ficients and relationships; (2)
computing average relationships very quickly within and between specified groups of individuals; (3)
computing average relatedness; (4) ancestral decomposition of the average or the individual
inbreeding coefficient; (5) anc
estral decomposition of the average coancestry; (6) optimizing matings
to minimize the average inbreeding coefficients in the next generation; (7) computing founder
equivalent, founder genome equivalent and effective number of non
-
founders; (8) computing
n
umerator relationship matrix, its Cholesky decomposition and its inverse; (9) providing useful
information on the structure of pedigrees

o

authors: Mehdi Sargolzaei (University of Guelph), Hiroaki Iwaisaki and Jean
-
Jacques Colleau

o

web/ftp: http://agrews.agr.
niigata
-
u.ac.jp/~iwsk/cfc.html

o

source code language: Visual C++

o

operating systems: MS
-
Windows(98/NT/XP)

o

executables:

o

reference: M Sargolzaei, H Iwaisaki, JJ Colleau (2006), "CFC: a tool for monitoring genetic diversity",
Proceedings of the 8th World Congre
ss on Genetics Applied to Livestock Production, CD
-
Rom comm.
N 27
-
28.



CHAPLIN

o

full name: Case
-
control HAPLotype INference package

o

version: 1.2.2

o

description: Chaplin is a software program for identifying specific haplotypes or haplotype features
that are a
ssociated with disease using genotype data from a case
-
control study.

o

authors: Richard Duncan, Michael Epstein, Glen Satten (Emory University)

o

web/ftp: http://www.genetics.emory.edu/labs/epstein/software/chaplin/index.html

o

source code language: FORTRAN90 (
CVF 6.6) with IMSL routines

o

operating systems: MS
-
Windows (2000/XP)

o

executables: chaplin.exe

o

reference: M Epstein, G Satten (2003), "Inference on haplotype effects in case
-
control studies using
unphased genotype data", American Journal of Human Genetics, 7
3(6):1316
-
1329

o

Satten, Epstein (2004), "Comparison of prospective and retrospective methods for haplotype
inference in case
-
control studies", Genetic Epidemiology, 27(3):192
-
201



CHECKHET

o

full name:

o

version: March'02 version

o

description: a program to detect

genetically abnormal subjects in a case
-
control sample based on
genotypes at multiple marker loci.

o

authors: Dave Curtis (Royal London Hospital, UK) (email: dcurtis@hgmp.mrc.ac.uk)

o

web/ftp: http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

o

http://www.
smd.qmul.ac.uk/statgen/software/dcurtis/chhet10.zip

o

source code language:

o

operating systems: MS
-
Windows, UNIX

o

executables:

o

reference: D Curtis, BV North, H Gurling, E Blaveri, PC Sham (2002), "A quick and simple method for
detecting subjects with abnormal
genetic background in case
-
control samples", Annals of Human
Genetics, 66:235
-
244.



CHECKMATRIX (other name: PY_MATRIX_2D)

o

full name:

o

version: v248

o

description: CheckMatrix serves as a visualization tool to validate constructed genetic maps.
CheckMatrix gen
erates graphical genotypes and two
-
dimensional heat plots of pairwise scores.
Visualization of regions with positive and negative linkage as well as of allele fraction per marker
simplifies genetic map validation without applying statistical approaches. Ch
eckMatrix works in
conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/

o

authors: Alexander Kozik (UC Davis)

o

web/ftp: http://www.atgc.org/XLinkage/

o

source code language: Python

o

operating systems:

o

executables:

o

reference:



CHIAMO

o

full name:

o

version: 0.2.1 (Oct 2007)

o

description: CHIAMO is a program for calling genotypes from the Affymetrix 500K Mapping chip. The
program allows for multiple cohorts which have potentially different intensity characteristics that
can lead to e
levated false
-
positive rates in genome
-
wide studies. The underlying model has a
hierarchical structure that allows for correlation between the parameters of each cohort. The output
files produced by CHIAMO feed directly into both the programs SNPTEST and I
MPUTE. CHIAMO was
used to call genotypes for the 7 genome
-
wide association studies carried out by the Wellcome Trust
Case
-
Control Consortium (WTCCC).

o

authors: Jonathan Marchini

o

web/ftp: http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html

o

source
code language:

o

operating systems:

o

executables:

o

reference: Marchini, Spencer, Teo, Donnelly (2007), "A Bayesian hierarchical mixture model for
genotype calling in a multi
-
cohort study",



CHIP2SPELL

o

full name:

o

version: 1.0.2 (September 2009)

o

description: Chip
2Spell aims to speed up the preparation of linkage data files passed on to the
Alohomora software for data from the Affymetrix or Illumina assays. Chip2Spell gathers the
information necessary to supplement the genotype data (such as the genetic map of the
markers
and the population
-
specific allele frequencies) from publicly available annoation files from
Affymetrix and Illumina. The program formats the genotype data for input into the Alohomora
program.

o

authors: Frederic Fournier (email: frederic.fournier@s
tatgen.org)

o

web/ftp: http://www.statgen.org/main/index.php/Downloads/Downloads

o

source code language: perl

o

operating systems: Linux, MS
-
Windows

o

executables:

o

reference:



CHROMOSCAN

o

full name:

o

version: 1.0

o

description: CHROMOSCAN is an implementation of a geno
me
-
based scan statistic that detects
genomic regions, which are statistically significant for targeted measurements, such as genetic
associations with disease, gene expression profiles, DNA copy number variations, as well as other
genome
-
based measurements
.

o

authors: Yan V Sun (email:yansun@umich.edu), Douglas M Jacobsen and Sharon LR Kardia (email:
kardiasoftware@umich.edu) (University of Michigan)

o

web/ftp: http://www.epidkardia.sph.umich.edu/software/chromoscan/

o

source code language: Java

o

operating systems
:

o

executables:

o

reference: Sun, Jacobsen, Kardia (2006), "ChromoScan: a scan statistic application for identifying
chromosomal regions in genomic studies", Bioinformatics, 22(23):2945
-
2947.

o

Sun, Levin, Boerwinkle, Robertson, Kardia (2006), "A scan statistic

for identifying chromosomal
patterns of SNP association", Genetic Epidemiology, 30(7):627
-
635.



CHROMOSEG

o

full name:

o

version: 1.0

o

description: A simulation program that simulates and plots (in real time) ancestral recombination
graphs. This is currently
primarily a teaching/educational tool.

o

authors: Eric C Anderson (email: eric.anderson@stanfordalumni.org)

o

web/ftp: http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm

o

source code language:

o

operating systems:

o

executables:

o

reference:



CHROMSCAN

o

ful
l name:

o

version: beta (December 11, 2006)

o

description: CHROMSCAN is a statistical based program for association mapping of disease genes. It
utilises the Malecot model and the linkage disequilibrium (LD) map for the candidate region to
analyse the genotype
s derive from large sample of matched cases and controls.

o

authors: A.R. Collins (University of Southampton)

o

web/ftp: http://www.som.soton.ac.uk/research/geneticsdiv/epidemiology/chromscan/

o

source code language:

o

operating systems:

o

executables:

o

reference:



CL
UMP

o

full name:

o

version:

o

description: Monte Carlo method for assessing significance of a case
-
control association study with
multi
-
allelic marker.

o

authors: Dave Curtis (Royal London Hospital, UK) (email: dcurtis@hgmp.mrc.ac.uk)

o

web/ftp: http://www.mds.qmw.a
c.uk/statgen/dcurtis/software.html

o

ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/statgen/dcurtis/

o

source code language: C

o

operating systems: MS
-
DOS

o

executables:

o

reference: Sham, Curtis (1995), Anna
ls of Human Genetics, 59:97
-
105;

online documentation



CLUSTAG

o

full name:

o

version: 2

o

description: hierarchical clustering and graph methods for selecting tage SNPs

o

authors: Sio Iong Ao, Michael K Ng (Dept of Mathematics, University of Hong Kong), Kevin Yip, David
Cheung (Dept of Computer
Science, University of Hong Kong), Pak Sham, Pui Yee Fong, Ian Melhado
(Genome Research Center, University of Hong Kong),

o

web/ftp: http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html

o

source code language: Java

o

operating systems:

o

executables:

o

reference: Ao,

Yip, Ng, Cheung, Fong, Melhado, Sham (2005), "CLUSTAG: hierarchical clustering and
graph methods for selecting tag SNPs", Bioinformatics, 21(8):1735
-
1736.



CMAP

o

full name: genetic and comparative maps

o

version: 0.06 (June 14, 2006)

o

description: CMAP is a we
b
-
based tool that allows users to view comparisons of genetic and physical
maps. The package also includes tools for curating map data.

o

authors: Ken Y Clark (email: kclark@cshl.org), Lincoln Stein (email: lstein@cshl.org), Doreen Ware
(email: ware@cshl.org
)

o

web/ftp: http://www.gmod.org/cmap/

o

http download: https://sourceforge.net/project/showfiles.php?group_id=27707

o

source code language: Perl

o

operating systems: UNIX (Solaris, FreeBSD), Linux

o

executables: cmap_admin.pl

o

reference: Ware et al. (2002), "Gramene
, a tool for grass genomics", Plant Physiology, 130:1606
-
1613.



COMBIN

o

full name:

o

version: 1.1

o

description: Designed for the construction of highly saturated linkage maps, based on BC1, DH,
Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supp
orted.

o

authors: Jaap Buntjer (Lab of Plant Breeding, Wageningen University. email:
jaap.buntjer@users.pv.wau.nl
)
, Herman van Eck (email: herman.vaneck@users.pv.wau.nl)

o

web/ftp: http://www.dpw.wau.nl/pv/pub/combin/

o

source code language: Visual Basic 5

o

operating systems: MS
-
Windows (95/98/NT)

o

executables:

o

reference:



COMDS

o

full name:

o

version:

o

description: for combined segregation and linkage analysis, incorporating severity and diathesis.

o

authors: NE Morton (University of Southampton, UK)

o

web/ftp: http://
cedar.genetics.soton.ac.uk/pub/PROGRAMS/comds

o

source code language: SUN FORTRAN (the command "fsplit" is needed)

o

operating systems: UNIX

(SunOS/..)

o

executables: list1,com1, comds (shell script)

o

reference: manual (N
ovember 1993)



COMPOSITELD

o

full name:

o

versi
on: 0.2.1 (December 2006)

o

description: A method to compute composite measures of linkage disequilibrium, their variances
and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is
unkown. An extension of Weir and C
ockerham (1989) to apply to multi
-
allelic loci.

o

authors: Daniel Schaid (Mayo Clinic)

o

web/ftp: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

o

source code language: R/S
-
PLUS

o

operating systems:

o

executables:

o

reference:



COPE

o

full name:
COllaborative Pedigree drawing Environment

o

version:

o

description: includes a Java program for drawing pedigrees and a standardized system for pedigree
storage. Unlike other existing pedigree programs, this software is particularly intended for
epidemiologis
ts in the sense that it allows customized automatic drawing of large numbers of
pedigrees and remote and distributed consultation of pedigrees.

o

authors: L Brun
-
Samarcq, S Gallina, A Philippi, F Demenais, G Vaysseix, E Barillot (email:
cope@infobiogen.fr
)

o

w
eb/ftp: http://www.infobiogen.fr/services/CoPE (closed)

o

source code language: Java

o

operating systems:

o

executables:

o

reference: Brun
-
Samarcq, et al, (1999) Bioinformatics, 15(4):345
-
346. [ full text (PDF) ].



COVIBD

o

full name:

o

version:

o

description: CovIBD ref
ines linkage analysis of affected sibpairs by considering attributes or
environmental exposures thought to affect disease liability. This refinement utilizes a mixture model
in which a disease mutation segregates in only a fraction of the sibships, with th
e rest of the sibships
unlinked. Covariate information is used to predict membership within the two groups corresponding
to the linked and unlinked sibships. The pre
-
clustering model uses covariate information to first form
two probabilistic clusters and t
hen tests for excess IBD
-
sharing in the clusters. The Cov
-
IBD model
determines probabilistic group membership by joint consideration of covariate and IBD values.

o

authors:

o

web/ftp: http://wpicr.wpic.pitt.edu/WPICCompGen/newcovibd/covibd.htm

o

source code lang
uage: R

o

operating systems:

o

executables:

o

reference: Devlin, Jones, Bacanu, Roeder (2002), "Mixture models for linkage analysis of affected
sibling pairs and covariates", Genetic Epidemiology, 22(1):52
-
65.

o

Devlin, Jones, Bacanu, Roeder (2002), "Reply to Olso
n", Genetic Epidemiology, 23(4):449
-
455.



CRIMAP

o

full name:

o

version: 2.4

o

description: constructing multilocus linkage map

o

authors: Phil Green (Univ. of Washington, email: phg@u.washington.edu
)

o

web/ftp: http://compgen.rutgers.edu/Crimap/

o

source code language
: C

o

operating systems: UNIX, MS
-
Windows(XP)

o

executables: crimap

o

referen
ce: Lander, Green (1987), Procee
dings of the National Academy of Sciences , 84:2363
-
2367.

o

documentation (version 2.4, 1990).

o

Tutorial (from biobase.dk)



CRIMAP
-
PVM

o

full name: CRIMAP with

Parallel Virtual Machine

o

version:

o

description: a parallel version of CRIMAP

o

authors: Tara Matise (email: matise@biology.rutgers.edu
)
, Mark Schroeder, Donald Chiarulli, Daniel
E. Weeks

o

web/ftp: http://compgen.rutgers.edu/multimap/crimappvm.html

o

source code

language: C, PVM

o

operating systems:

o

executables:

o

reference: Matise,

Schroeder, Chiarulli, Weeks, (1995) Human Heredity, 45:103
-
116.



CROSSFIND (other names: BREAKPOINT, BPT)

o

full name:

o

version: October 1995

o

description: software for detecting and displayin
g well
-
characterized meiotic breakpoints in human
family data. another program, CRIMAP, is used.

o

authors: J. Attwood (Sanger Centre, email: ja1@sanger.ac.uk)

o

web/ftp: http://www.gene.ucl.ac.uk/public
-
files/packages/jattwood/

o

source code language: C

o

operati
ng systems: UNIX(SunOS)

o

executables:

o

reference: Attwood, Povey (1996), Annals of Human Genetics, 60:487
-
498.



CYRILLIC

o

full name:

o

version 3 (October 1999)

o

description: (version 3) pedigree drawing with fully integrated risk analysis and support for industry

standard databases (MS Access and Corel Paradox). designed for genetic counselors and others who
work with patients. if you use genetic marker data you need Cyrillic 2. (version 2) this version of
Cyrillic draws pedigrees, works with genetic marker data,
lets you do haplotyping and allows exports
to a range of linkage analysis packages.

o

authors: Cherwell Scientific Publishing and Cyril Chapman (email: cyrillic@cherwell.com
)

o

web/ftp: http://www.cyrillicsoftware.com

o

http://www.cyrillicsoftware.com/download/downloads.htm

o

source code language: Visual C++

o

operating systems: MS
-
Windows (95/98/NT)

o

executables:

o

reference: Chapman (1990), American Journal of Medical Genetics, 36:155
-
160.

o

availability: commercial v2.1 (US$599
/379 UK pounds/570 euros), 3 (US$769/479 UK pounds/725
euro), upgrades from v2.1 to v3 (US$299), upgrades from v2 to v3 (US$399),

o

vender: Cyrillic Software, UK; Exeter Software (USA reseller)



DCHIP LINKAGE

o

full name:

o

version:

o

description:

o

authors: Igor Ley
kin, Cheng Li (Harvard University)

o

web/ftp: http://www.biostat.harvard.edu/complab/dchip/snp.htm

o

http://www.biostat.harvard.edu/~ileykin/accessory.htm

o

source code language: C++

o

operating systems: MS
-
Windows

o

executables:

o

reference: Leykin et al. (2005), "Co
mparative linkage analysis and visualization of high
-
density
oligonucleotide SNP array data", BMC Genetics, 6:7.

o