http://www.datam0nk3y.org/hyphy/ 2012-05-18T16:29:37-07:00 http://www.datam0nk3y.org/hyphy/ http://www.datam0nk3y.org/hyphy/lib/images/favicon.ico text/html 2010-05-28T11:41:32-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=art_fy_poon&rev=1275072092&do=diff Art FY Poon Associate Research Scientist, Bioinformatics BC Centre of Excellence in HIV/AIDS Vancouver, British Columbia 603-1081 Burrard St Canada V6Z 1Y6 E-mail: email Art Research Interests I study the molecular evolution of viruses, in particular by developing computational or experimental techniques to elucidate the biological constraints from the signature of evolutionary processes on genetic sequence data. I also collaborate with other groups in developing computational tools fo… text/html 2010-02-09T14:22:06-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=cms&rev=1265754126&do=diff We are working on populating this tutorial, but first we must finish the manuscript describing the method. Thanks for your patience! text/html 2010-02-03T17:48:14-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=datamonkey&rev=1265248094&do=diff * Codon Model Selection: how to interpret the results of GA-based codon model selection implemented in Datamonkey text/html 2010-05-28T12:00:34-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=distancematrixmpi.bf&rev=1275073234&do=diff ChoiceList (distanceChoice, “Distance Computation”,1,SKIP_NONE, “Distance formulae”,”Use one of the predefined distance measures based on data comparisons. Fast.”, “Full likelihood”,”Estimate distances using pairwise MLE. More choices but slow.”); if (distanceChoice < 0) { return 0; } ChoiceList (dataType,”Data type”,1,SKIP_NONE,”Nucleotide/Protein”,”Nucleotide or amino-acid (protein).”, “Codon”,”Codon (several available genetic codes).”); if (dataType<0) { … text/html 2011-10-22T11:51:27-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=download&rev=1319309487&do=diff Available HyPhy versions * Developmental. Presently, HyPhy is undergoing a major rewrite leading up to version 2.0. For the latest features and maximum speed, download on of the current builds. This is recommended for most users. * Latest v1.0 release. The latest 1.0 release was compiled on May 12th, 2008 and has not been updated since then. You may want to download this version if you need the functionality not yet fully ported to v2.0 (this is rare). text/html 2009-10-08T11:42:23-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=gildredmove&rev=1255027343&do=diff * Rolling an empty cluster cabinet down 5 city blocks and getting a lot of really odd looks from the drivers. [Rolling an empty cluster cabinet down 5 city blocks and getting a lot of really odd looks from the drivers.] * Taking a well-deserved break at the destination. text/html 2010-05-10T11:44:47-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=hbf&rev=1273517087&do=diff A collection of various HyPhy batch language (HBL) files. A list of available HBL text/html 2010-05-27T16:28:17-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=hyphy_news&rev=1275002897&do=diff This list is overdue by about 10 years... We'll make an effort to maintain it. A list of various add-on files (not a part of the distribution) can also be found here: HyPhy Batch Files ---------- * 2010-May-27 [AFYP]. Tweaked DistanceMatrix.bf so that it can handle tens of thousands of sequences at once in an MPI environment without barfing. See my page for attachment. text/html 2011-07-27T13:41:07-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=jason_a_young&rev=1311799267&do=diff Jason A. Young Assistant Adjunct Professor Department of Medicine University of California, San Diego 220 Dickinson St, Suite A San Diego, CA 92103 Phone: +1 619 543 8073 Fax : +1 619 543 5066 E-mail: email Jason text/html 2012-03-02T17:28:38-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=joel_o_wertheim&rev=1330738118&do=diff Joel O. Wertheim Postdoctoral Research Fellow Department of Pathology University of California, San Diego 220 Dickinson Street, Suite A San Diego, CA 92103 Phone: +1 619 543 5069 E-mail: email Joel I aim to understand the evolution and emergence of pathogenic RNA viruses (e.g. HIV, influenza A virus, measles virus, Ebola virus, etc.) using phylogenetics and other computational tools. I also study these viruses to learn more about evolutionary processes in general. In addition, I am int… text/html 2011-06-30T15:08:10-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=martin_d_smith&rev=1309471690&do=diff Martin D. Smith Graduate Student Bioinformatics and Systems Biology Graduate Program Department of Bioengineering University of California, San Diego 220 Dickinson Street, Suite A San Diego, CA 92103 E-mail: email Martin 2010- : PhD, Bioinformatics and Systems Biology, University of California, San Diego 2006-2010: BS, Biology, minor in Informatics and Computer Science. University of California, Irvine. text/html 2011-08-03T18:59:34-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=mathieu_fourment&rev=1312423174&do=diff Mathieu Fourment Postdoctoral Research Fellow Department of Pathology University of California, San Diego 220 Dickinson Street, Suite A San Diego, CA 92103 Phone: +1 619 543 5625 Email: mfourment@ucsd.edu Website: mateo.fourment.free.fr phylogenetics.tk text/html 2009-06-03T18:54:00-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=register&rev=1244080440&do=diff If you have registered before or do not want to register at this time, proceed directly to the Download page. Otherwise, please fill out the following form. <database USERS basefilter=“id gt 4”> EMAIL, integer,, readonly aliasing=“count(email)” </database> text/html 2011-04-26T10:01:56-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=sergei_l_kosakovsky_pond&rev=1303837316&do=diff Sergei L Kosakovsky Pond Assistant Adjunct Professor Department of Medicine University of California, San Diego 220 Dickinson St, Suite A San Diego, CA 92103 Phone: +1 619 543 8898 Fax : +1 619 543 5066 E-mail: email Sergei [CV] Brief Academic Biography Following formal undergraduate training in computer science (at Kiev State University, Ukraine), I received a PhD from the interdisciplinary program in Applied Mathematics at the University of Arizona. My theoretical graduate research … text/html 2010-05-19T16:14:42-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=slkp_hbl_batch_wrapper&rev=1274310882&do=diff HBL, SergeiLKosakovskyPond, MPI, Wrappers These files provide a simple example of how to apply the same analysis to a collection of files references to in a path list file using MPI, collect custom outputs and write them to a HyPhy parse-able file (associative array). Please modify accordingly; the current file fits 3 different codon models using AnalyzeCodonData.bf to a collection of files. text/html 2010-05-19T16:15:21-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=slkp_hbl_codon_simulator&rev=1274310921&do=diff HBL, SergeiLKosakovskyPond, Simulation The purpose of these files is to simulate many replicates of codon data under the MG94 x REV model of sequence evolution. Both synonymous and non-synonymous rates can vary from site to site, and there can be multiple omega classes in a substitution matrix. There are three files text/html 2010-05-19T17:01:05-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=slkp_hbl_pref_attachment&rev=1274313665&do=diff HBL, SergeiLKosakovskyPond, MPI, Wrappers A simple batch file (see the source for user configurable parameters; top of the file) which simulates a network using the model of preferential attachment on N nodes, and subsamples one or more subnetwork on M < N nodes from it. Sampling can be random or biased towards oversampling clusters. In addition to summary statistics, adjacency matrices for each subsample are written out if requested. text/html 2011-06-09T16:09:29-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=start&rev=1307660969&do=diff HyPhy.org is home to the HyPhy molecular evolution and statistical sequence analysis software package developed by members of the Viral Evolution Group at the School of Medicine at UCSD and collaborators at other institutions. HyPhy is a feature rich and mature (in development since 1997), feature rich, scriptable and fast maximum likelihood sequence analysis software platform with over 6000 registered users and over 500 citations in peer reviewed literature. text/html 2011-07-13T12:17:14-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=steven_weaver&rev=1310584634&do=diff Steven Weaver Programmer/Analyst Department of Medicine University of California, San Diego 220 Dickinson St, Suite A San Diego, CA 92103 Phone: +1 619 672 7031 E-mail: email Steven text/html 2009-10-08T15:35:32-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=team&rev=1255041332&do=diff HyPhy contributors outside UCSD Spencer V Muse Professor of Statistics at North Carolina State University Spencer's lab at NCSU Simon DW Frost University Senior Lecturer, Cambridge University Simon's lab at Cambridge Art FY Poon Associate Research Scientist, Bioinformatics BC Centre for Excellence in HIV/AIDS text/html 2011-10-07T15:54:03-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=veg&rev=1318028043&do=diff UCSD viral evolution group is comprised of members of several departments from the UCSD School of Medicine. The primary areas of our basic research efforts are statistical evolutionary analysis of pathogens and computational biology in translational research. We apply the methods and software tools that we develop to the study of HIV-1, Influenza A virus and other pathogens. text/html 2011-04-04T11:09:38-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=veg_meeting_schedule&rev=1301940578&do=diff Mondays are Science meetings where we will cycle among the academics in the group to discuss current work and solutions to problems. Time: Mondays at 1 pm Location: 1st Floor AVRC Conference Room Mondays are also Standup meetings where each person talks about what they've done in the past week and what's coming up on the horizon. Time: Mondays at 2:30 pm Location: 1st Floor AVRC Conference Room Wednesdays are Journal Clubs. All are welcome to attend and present. This is an oppo… text/html 2010-07-29T16:02:51-07:00 http://www.datam0nk3y.org/hyphy/doku.php?id=wayne_delport&rev=1280444571&do=diff Wayne Delport Assistant Project Scientist Department of Pathology University of California, San Diego 150 W Washington St, Ste 100 San Diego, CA 92103 Phone: +1 619 543 8899 Fax : +1 619 543 4761 E-mail: email Wayne My interests lie in using and developing computational tools for modeling evolution of viruses and other organisms.