Software Available in Open Systems
|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|
|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|
|gas2||Is installed. Its test data is available as gas2.dat|
|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: email@example.com 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:|
|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.|
|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 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.
|subversion||V1.6.13 is avaiable|
|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)|