Software

Software Available in Open Systems

Program Information/Documentation
454 454 Sequencing tools
act Analysis of Complex Traits, a group of programs we wrote.
allegro Version 2.0f is available as of April 2011. Documentation is available too.

Version 1.2c is also available, in case anyone needs it. Its documentation is also posted.

ancestrymap Version 2-rel is available as of April 2011. User should go to the author's Web site for documentation.
APT Affymetrix Power Tools version 1.15.0. This group of programs is installed on Linux servers
beaglecall Version 0.9.4.
bimbam Version 1.0 is available as of February 2, 2013. It was built to support parallel computation with Open-MPI wrapper.
birdsuite Version 1.5.5 is installed on our Linux servers.
cage Cohort Analyss for Genetic Epidemiology. Available on Solaris servers
consed consed-16.0 for sequence analysis.
eigenstrat Eigenstrat-2.0 is available - in Linux environment only though.
erpa Old linkage program
fastlink version 2.51
gas2 Is installed. Its test data is available as gas2.dat
genomeSIMLA Simulation program
GenomeStudio Free program from Illumina - available on our Windows Server
ghm This is gh2 that does MOD score. Documentation is available here. Windows version is also available.
gnuplot version 5.0.3 available as of June 17, 2016
gpc Version 20060325 is ailable as of April 2011. This is a GNU Pascal compiler
gtool GWAS program, v0.6.6
impute2 Available on Linux server, upgraded to v2.1.0 as of august 2010.
Ingenuity Per Thomas H. Hampton,
I have used Ingenuity pretty regularly for about 10 years. We mostly use it for gene expression analysis, and it ‘
is helpful to us that Ingenuity is interoperable with CLC Genomics Workbench, which means that one can 
actually carry out am analysis of gene expression starting with raw sequence reads and go all the way to 
a functional analysis in one, smooth motion.

Of particular interest to me has been the emergence of the ability to use differential gene expression to 
infer upstream regulation activity as well as regulation effects. For example, one might submit a set of
gene regulation scores and Ingenuity might predict that those scores are consistent with exposure to
arsenic, and that the predicted effect of the gene expression would be reduced T cell migration. That 
kind of thing actually happens..

I have had very few questions, over the years, about how to get Ingenuity to do things. The interface 
is consistent and intuitive.  

We have a license that we are contractually prohibited from sharing. We are, however,
at liberty to participate in analysis as collaborators, and have done this in the past 
on projects where our skills add value to the research.

Trial licenses are free, and I recommend it for Dartmouth general use if there is 
sufficient interest. 

jPAP Pedigree Analysis Package for Java
Linkage Programs Good old fashioned linkage programs
LIVEServer Coupling program for X-Win32, to create a LIVE session on Windows desktops -- rendering the entire Desktop
loki Version 2.3.1 is available
mach Markov Chain based haplotyper
mega2 Manipulation Environment for Genetic Analyses
merlin Another fancy linkage program
metal Meta Analysis Helper
mqls Case-Control association testing with related individuals...
MySQL Version 5 available
ncftp Version 3.2.2 available
nose Version 0.11.1 available
numpy Version 1.2.0 available
openmpi Version 1.4.1 available
Partek Partek Genomics Suite 6.6 is available as of 8/8/2012. Follow download link to obtain software, then use this syntax to activate your copy: 27004@rclserv1.dartmouth.edu after installation. This package is available in Windows, NacOS, and Linux, both 32-bit and 64-bit.

Alternatively, you can use Partek Genomic Suite on morgan2 if you have an account. Simply login to morgan2 in X-Win32, then type partek to fire up its Java GUI

pap Currently avaiable in version 7.1. FORTRAN source files are available. Read its documentation in PDF format.
Pathway Studio Register yourself at the vendor website, and you will have a username and a password to login and start using this web-based software
pedcheck Program for detecting marker typing incompatobilities inpedigree data
perl Version 5 available
phrap DNA sequencing tools, release 0.990329
plink Open source program for Whole Genome Association Analysis. Read its documentation in PDF format.
polyphred Version 6.11 is avaiable . Read documentation in HTML format.
probABEL Genetic analysis library in R, version 0.1.3
python Version 2.6 available
R R is installed on all UNIX/Linux servers. In most cases, these additional modules are also available:

BayesMendel : It's also available for Windows.

rendomForest, and its documentation.

rar rar v 3.8.0
relpair Infers relationships of pairs of individuals based on genetic marker data. Version 2.0.1 is available as of January 2010.

Information and sample files are available.

S+ Splus-8.1.1 is available as of April 2010. It comes in several flavors, RedHat Linux, SUN/Solaris, and Windows. Documentation is available.
SAGE SAGE 6.0.1 is installed on mdamalecot. mdahaldane, tukey, and wright. Its documentation is also available in PDF format. PDF files are also available at version 3.1 level.

Available executables are merged from versions 6.0.1 and 3.1.

Samba Samba is installed on morgan2. You can treat your UNIX files like a network share from your PC. More documentations are localized here.
SAS 9.4 Available on morgan2 (RedHat Linux Server)

Read SAS 9.3 documentation on-line.

There's also a really good On-Line Tutor available! (The Tutor likes Netscape better...)

SAS 9.2 documentation is available, both on SAS's Web Site, and on Local Web site (updated 05/10/2010).

Pure PDF Files are also available.

SAS Enterprise Guide is available for Windows users with an UNIX account on morgan2. This is a Windows GUI program supported by SAS installed on a Server. Read on for details...

simped Simped quickly generates haplotype...
simwalk Stochastic Statistical Analysis Qualitative Traits, v2
SnapGene SnapGene allows you to make DNA maps and design primers. It offers easy ways to plan, visualize, and document your molecular biology procedures, including a range of cloning and PCR manipulations.

Thanks Arminja.N.Kettenbach@dartmouth.edu for the above description

snptest Analysis of single SNP association in genome-wide studies
solar Solar 2.1.2 is installed on cedric (May 6th, 2004). Documentation is available.
Solaris Openrating System Solaris 10 Documentation downloaded and installed here for local use (as of March 2011.)
Solaris 11 is already out -- but there is no plan to upgrade yet.
structure v 2.2.3
subversion V1.6.13 is avaiable
superlink v 1.7
SUN Studio A collection of compilers are available on SUN Solaris 10 environment
SVS HelixTree 6.1.0 documentation available, in HTML format, or PDF format

HelixTree 7.1.1 (64-bit) Documentation came in DPF format.

SVS V7.6.0 available (01/30/2012).

We have two floating license at Dartmouth

swig This could be some prerequiste to subversion. V 1.3.36 is installed
tlink Linkage with Imprinting
valgrind Valgrind is an instrumentation framework for building dynamic analysis tools. V 3.3.1 is installed
vitesse Linkage program. V2 is available
UNIX Primer Basic UNIX skills
UNIX Training For those who never used UNIX -- start from here.
X-Win32 About X-Win32 (may require Dartmouth VPN to view)