This is a list of all software available on the helix Please see the special software list for the alpha compute nodes (what's that anyway?) If you encounter any problems or need any additional programs please do not hesitate to contact hpcc@fieldmuseum.org jump to: General sequence analysis tools (EMBOSS, etc.) Alignment Tools (ClustalW, MULTICLUSTAL, etc.) Phylogenetic Analysis (PAUP*, Bambe, etc.) Hypothesis Testing, Comparative Method, Population Genetics (Modeltest, r8s, etc.) Graphical Tree Viewers General Sequence Analysis Tools EMBOSS 0.0.4 Go to the EMBOSS home page to view program descriptions and their commands. The EMBOSS quick guide is available in pdf format or in postscript format. Teiresias, Musca, Delphi Pattern recognition, multiple alignment and protein database tools developed by the IBM Bioinformatics Research Group. Local online information (including tutorials) is available. Phy2Nex (Phylip to Nexus translator) At the prompt, type:   phy2nex This program is part of SeqGen, so online help may be found at the SeqGen Home Page. Alignment Tools ClustalW 1.8 At the prompt, type:   clustalw ClustalW Online Help MULTICLUSTAL At the prompt, type:   MULTICLUSTAL.sh Multiclustal Help File I recommend creating a new folder for your MULTICLUSTAL analysis as it creates many files. You will also need to have the following files in the directory/folder where you plan to run MULTICLUSTAL: box_dna.par box_dna.sim box_pep.par box_pep.sim clust160.sim positive.sim strong.sim Malign 1.99 At the prompt, type:   malign Malign Readme File Phylogenetic Analysis BAMBE 2.02 beta At the prompt, type:   bambe BAMBE Home Page Associated programs you will need: MeanSD - at the prompt, type:   meansd Summarize - at the prompt, type:   summarize Paup*4, beta version 7 At the prompt, type:   paup And check out the special tutorial on how to use Paup! Paup* Home Page. MrBayes 1.11 at the prompt typ: mb or use the following syntax: mb < runfile > out & this tells UNIX to start MrBayes and to feed it the runfile, to send all screen output to the file out, and put the process in background. This is similar to running Paup (see above). And check out the MrBayes Home Page, where you can get the newest Manual. MolPhy 2.3b3 To run NJDIST, type:   njdist To run NUCML, type:   nucml To run NUCST, type:   nucst To run PROTML, type:   mprotml To run PROTST, type:   protst To run TOTALML, type:   totalml There is no documentation available from the author. PAML 3.0b To run BASEML, type:   baseml To run BASEMLG, type:   basemlg To run CODEML, type:   codeml To run PAMP, type:   pamp To run MCMCTREE, type:   mcmctree To run EVOLVER, type:   evolver PAML Home Page Phylip The Phylip Home Page has a complete list of programs, their commands, and documentation. Phyloquart 1.3 Phyloquart Main Help File To run ADDQUART, type:   addquart AddQuart help file To run DISTQUART, type:   distquart DistQuart help file To run PARCIQUART, type:   parciquart ParciQuart help file To run QSTAR, type:   qstar QStar help file To run TREE-POP, type:   tree-pop Tree-Pop help file Hypothesis Testing, Comparative Method, Molecular Population Genetics DNArates At the prompt, type:   DNArates DNARates help file ModelTest 3 At the prompt, type:   modeltest3 Modeltest Home Page SeqGen 1.10 At the prompt, type:   seq-gen SeqGen Home Page discrete 1.0.1a At the prompt, type:   discrete Discrete Readme File Discrete Postscript File SNAP (Synonymous Nonsynonymous Analysis Program) At the prompt, type:   SNAP.pl SNAP home page Associated programs: SNAP Statistics (to run, type:   SNAPstats); SNAP Codons plot (to run, type:   codons-xyplot.pl) r8s At the prompt, type:   r8s You will then obtain a prompt like: r8s> For help, at the r8s prompt, type ? r8s home page Derange 2.0 At the prompt, type:   derange2 Derange Help File Graphical Tree Viewers (requires X-Window software on your desktop computer) NJPlot Requires X windows interface. At the prompt, type:   njplot NJPlot Home Page Unrooted Requires X windows interface. At the prompt, type:   unrooted Unrooted Home Page TAAR Requires X windows interface. At the prompt, type:   taar TAAR Home Page X-Window Software Some UNIX programs provide or require a graphical interface. To make use of this interface, you will need an X server running on your desktop computer. The X server takes all input from your keyboard and mouse, and sends it to the UNIX server, which then relays it to the X client on the server. It will appear as if the X client were actually running on your desktop computer. As Computing Services does not support any of this software, please consult with Stefan Zoller before making any purchases. MicroImages X server (Free for Mac, $25 for Windows) PowerLAN's eXodus (formerly White Pine's eXodus) - commercial software for Mac UniPress Exceed (Formerly Hummingbird) - commercial software for Windows Software on the alpha compute nodes On the alpha compute nodes is only a reduced set of software available (more will be added later): - PAUP*4b7 At the prompt, type:   paup And check out the special tutorial on how to use Paup! Paup* Home Page. - Bambe 2.02 beta At the prompt, type:   bambe BAMBE Home Page Associated programs you will need: MeanSD - at the prompt, type:   meansd Summarize - at the prompt, type:   summarize - ClustalW 1.8 At the prompt, type:   clustalw ClustalW Online Help - MolPhy 2.3b3 To run NJDIST, type:   njdist To run NUCML, type:   nucml To run NUCST, type:   nucst To run PROTML, type:   mprotml To run PROTST, type:   protst To run TOTALML, type:   totalml There is no documentation available from the author.