Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00249 NAME QC DOMAIN Sequence analysis DOMAIN Statistical significance DESCRIPTION The qc program calculates the hexanucleotide frequences or any DESCRIPTION other n from 2-x in dna from separate groups and then does a DESCRIPTION liklihood ratio test on the maximum liklihood under the binomial DESCRIPTION model that the two samples are the same or different using a DESCRIPTION chi-square statistic. AUTHOR Owen White (owhite@tigr.org), Ted Dunning (ted@nmsu.edu) RA White O., Dunning T.; RT "Accurate methods for the statistics of surprise and RT coincidence."; RL in press (?). RA White O., Dunning T., Sutton G., Adams M., Venrer J.C., Field C.; RT "A quality control algorithm for DNA sequencing projects."; RL Nucleic Acids Res. 21:3829-3838(1993). RX Medline; 93376509. RX SeqAnalRef; WHIO9301. ADDRESS The Institute for Genomic Research ADDRESS 932 Clopper Road ADDRESS Gaithersburg, MD 20878, USA CONTACT - SITE ftp anonymous ftp.tigr.org SITE Directory /pub/qc SITE-CONTACT - OS Unix LANGUAGE C, flex VOLUME - REQUIRES the lexical interpreter 'flex' from GNU COMMENTS GNU flex bcan be found at prep.ai.mit.edu Directory /pub/gnu AC BC00284 NAME RDF2 DOMAIN Statistical significance DESCRIPTION improved version of RDF program with all DESCRIPTION three scoring methods (now includes local, DESCRIPTION or window, shuffle routine) AUTHOR - RT - ADDRESS U. of Virginia Dept. of Biochemistry CONTACT - SITE ftp anonymous ftp.virginia.edu SITE Directory /pub/fasta = fasta(version number) SITE-CONTACT William Pearson wrp@virginia.edu OS all LANGUAGE - VOLUME - AC BC00391 NAME BCM Search Launcher DOMAIN WWW server DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Restriction maps DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis SERVER http://www.hgsc.bcm.tmc.edu/SearchLauncher/ DESCRIPTION The BCM Search Launcher is an integrated set of World- DESCRIPTION Wide Web (WWW) pages that organize molecular biology- DESCRIPTION related search and analysis services available on the DESCRIPTION WWW by function, and provide a single point-of-entry for DESCRIPTION related searches. The Protein Sequence Search Page, for DESCRIPTION example, provides a single sequence entry form for DESCRIPTION submitting sequences to WWW servers that provide remote DESCRIPTION access to a variety of different protein sequence search DESCRIPTION tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, DESCRIPTION PROSITE, and BLOCKS searches. Other Launch pages provide DESCRIPTION access to 1) nucleic acid sequence searches, 2) multiple DESCRIPTION and pairwise sequence alignments, 3) gene feature searches, DESCRIPTION 4) protein secondary structure prediction, and 5) DESCRIPTION miscellaneous sequence utilities (e.g., 6-frame DESCRIPTION translation). The BCM Search Launcher also provides a DESCRIPTION mechanism to extend the utility of other WWW services by DESCRIPTION adding supplementary hypertext links to results returned DESCRIPTION by remote servers. For example, links to the NCBI's DESCRIPTION Entrez database and to the Sequence Retrieval System DESCRIPTION (SRS) are added to search results returned by the NCBI's DESCRIPTION WWW BLAST server. These links provide easy access to DESCRIPTION auxiliary information, such as Medline abstracts, that DESCRIPTION can be extremely helpful when analyzing BLAST database DESCRIPTION hits. For new or infrequent users of sequence database DESCRIPTION search tools, we have pre-set the default search parameters DESCRIPTION to provide the most informative first-pass sequence DESCRIPTION analysis possible. We have also developed a batch client DESCRIPTION interface for Unix and Macintosh computers that allows DESCRIPTION multiple input sequences to be automatically searched as DESCRIPTION a background task, with the results returned as individual DESCRIPTION HTML documents directly to the user's system. AUTHOR Randall F. Smith, Brent A. Wiese, Mary K. Wojzynski, AUTHOR Daniel B. Davison , and Kim C. Worley RA Smith R.F., Wiese B.A., Wojzynski M.K., Davison D.B., Worley K.C.; RT "BCM Search Launcher--An integrated interface to molecular RT biology database search and analysis services available on RT the World-Wide Web."; RL Submitted. ADDRESS Randall F. Smith, Ph.D. ADDRESS Department of Molecular and Human Genetics, T-921, ADDRESS Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Tel: +1 (713) 798-4735 Fax: +1 (713) 798-5386 CONTACT rsmith@bcm.tmc.edu CONTACT kworley@bcm.tmc.edu SITE WWW Server at URL http://www.hgsc.bcm.tmc.edu/SearchLauncher/ SITE-CONTACT rsmith@bcm.tmc.edu SITE WWW Server at URL http://dot.imgen.bcm.tmc.edu:9331/downloads/software/batch_client.html SITE give information about the downloads SITE ftp anonymous dot.imgen.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00435 NAME BEAUTY DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Database and analysis DOMAIN Searching databases DOMAIN Statistical significance DOMAIN Comparative analysis DOMAIN WWW server DESCRIPTION BEAUTY (BLAST Enhanced Alignment Utility) is an enhanced DESCRIPTION version of the NCBI's BLAST database search tool that DESCRIPTION facilitates identification of the functions of matched DESCRIPTION sequences. We have created new databases of conserved DESCRIPTION regions and functional domains for protein sequences in DESCRIPTION the NCBI's Entrez database, and BEAUTY allows this DESCRIPTION information to be directly incorporated into BLAST search DESCRIPTION results. A Conserved Regions Database, containing the DESCRIPTION locations of conserved regions within Entrez protein DESCRIPTION sequences, was constructed by 1) clustering the entire DESCRIPTION database into families, 2) aligning each family using our DESCRIPTION PIMA multiple sequence alignment program, and then DESCRIPTION 3) scanning the multiple alignments to locate the DESCRIPTION conserved regions within each aligned sequence. A DESCRIPTION separate Annotated Domains Database was constructed by DESCRIPTION extracting the locations of all annotated domains and DESCRIPTION sites from sequences represented in the Entrez, PROSITE, DESCRIPTION BLOCKS, and PRINTS databases. BEAUTY performs a BLAST DESCRIPTION search of those Entrez sequences with conserved regions DESCRIPTION and/or annotated domains. BEAUTY then uses the DESCRIPTION information from the Conserved Regions and Annotated DESCRIPTION Domains databases to generate, for each matched sequence, DESCRIPTION a schematic display that allows one to directly compare DESCRIPTION the relative locations of 1) the conserved regions, DESCRIPTION 2) annotated domains and sites, and 3) the locally-aligned DESCRIPTION regions matched in the BLAST search. In addition, BEAUTY DESCRIPTION search results include World-Wide Web hypertext links to DESCRIPTION a number of external databases that provide a variety of DESCRIPTION additional types of information on the function of matched DESCRIPTION sequences. This convenient integration of protein DESCRIPTION families, conserved regions, annotated domains, alignment DESCRIPTION displays, and World-Wide Web resources greatly enhances DESCRIPTION the biological informativeness of sequence similarity DESCRIPTION searches. Beauty searches can be performed remotely on DESCRIPTION our system using the "BCM Search Launcher" World-Wide-Web pages AUTHOR Kim C. Worley, Brent A. Wiese, and Randall F. Smith RA Worley K.C., Wiese B.A., Smith R.F.; RT "BEAUTY: An enhanced BLAST-based search tool that RT integrates multiple biological information resources RT into sequence similarity search results."; RL Genome Research 5:173-184 (1995). ADDRESS Kim C. Worley, Ph.D. ADDRESS Department of Molecular and Human Genetics ADDRESS T-929, Baylor College of Medicine ADDRESS One Baylor Plaza, Houston, TX 77030, USA ADDRESS Phone: +1 (713) 798-8292 FAX: +1 (713) 798-5386 CONTACT kworley@bcm.tmc.edu CONTACT brent@bcm.tmc.edu CONTACT rsmith@bcm.tmc.edu SITE WWW server at URL http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html SITE-CONTACT rsmith@bcm.tmc.edu SITE ftp anonymous gc.bcm.tmc.edu for a batch client SITE Directory /pub/software/search-launcher OS Unix and Macintosh for the batch client LANGUAGE Perl (on Unix), AppleScript (on Macintosh) VOLUME - REQUIRES MacTCP on Macintosh and AppleScript, Perl on Unix AC BC00437 NAME MIM DOMAIN Genetic Linkage software DOMAIN Genetic and Physical Mapping DOMAIN Statistical significance DOMAIN Multivariate analysis DESCRIPTION MIM is a program to implement the Multipoint IBD method for DESCRIPTION partitioning genetic variance of quantitative traits to DESCRIPTION specific chromosomal regions using data on nuclear families. AUTHOR David E. Goldgar, Cathryn M. Lewis, Khosrow Gholami, AUTHOR Edward N. Kort RA Goldgar D.E.; RT "Multipoint analysis of human quantitative genetic variation."; RL Am. J. Hum. Genet. 45:957-967(1990). RA Goldgar D.E., Oniki R.O.; RT "Comparison of a multipoint identity by descent method with RT parametric multipoint linkage analysis for mapping quantitative traits."; RL Am. J. Hum. Genet. 50:598-606(1992). ADDRESS Cathryn Lewis, Ph.D. ADDRESS Genetic Epidemiology ADDRESS 391 Chipeta Way, D2 ADDRESS Salt Lake City, UT 84108, USA CONTACT edward@episun2.med.utah.edu SITE ftp anonymous morgan.med.utah.edu SITE Directory /pub/Mim SITE-CONTACT - OS UNIX LANGUAGE C VOLUME 250K bytes REQUIRES - COMMENTS Copies of the program may be obtained COMMENTS by contacting Edward Kort at edward@episun2.med.utah.edu AC BC00467 NAME ABaCUS DOMAIN Statistical significance DOMAIN exon-protein correspondence analysis DESCRIPTION If you are interested in the possible DESCRIPTION involvment of introns in protein gene evolution, this may DESCRIPTION be of interest. ABaCUS is a no-frills program designed to DESCRIPTION investigate the significance of some types of possible DESCRIPTION correspondence between exons and units of protein DESCRIPTION structure. This type of analysis takes the form of an DESCRIPTION attempt to eliminate the reference ("null") hypothesis that DESCRIPTION the correspondence seen in the observed data is no greater DESCRIPTION than expected by chance. The program continues to be DESCRIPTION updated to allow more complex correspondence metrics and DESCRIPTION reference gene models. There are also routines to simulate DESCRIPTION the effects of deletion and so-called "sliding" of DESCRIPTION introns. AUTHOR Stoltzfus A. RA Stoltzfus A., Spencer D.F., Doolittle, W.F.; RT "Methods for evaluating exon-protein correspondences."; RL Comp. Appl. Biosci. 11(5):509-515(1995). RA Stoltzfus A., Spencer D.F., Zuker M., Logsdon J.M., RA Doolittle, W.F.; RT "Testing the Exon Theory of Genes: the Evidence from RT Protein Structure."; RL Science 265:202-207(1994). ADDRESS Department of Biochemistry ADDRESS Dalhousie University ADDRESS Halifax, Nova Scotia B3H 4H7 Canada CONTACT arlin@is.dal.ca SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /pub/evolve/abacus SITE-CONTACT Archive@Bio.Indiana.Edu OS UNIX, MacOS, DOS LANGUAGE ANSI C VOLUME 100 Kbytes REQUIRES C compiler COMMENTS ABaCUS should be easy to compile on any platform with an COMMENTS ANSI C compiler. Specific instructions are included in COMMENTS the readme file and the help document in the ABaCUS COMMENTS distribution. AC BC00469 NAME OSA DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Epidemiology DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION OSA is a program to find, within an alignment of DESCRIPTION large sequences, those regions with an informative content DESCRIPTION similar to the displayed by the whole alignment and select, DESCRIPTION among them, the shortest empiricaly significant ones. The use of DESCRIPTION these short regions, instead of the larger ones, can save a DESCRIPTION considerable amount of time and resources in molecular screening DESCRIPTION or molecular epidemiology studies. AUTHOR Maria Jesus Martin, Joaquin Dopazo RA Martin M.J., Gonzalez-Candelas F., Sobrino F., Dopazo J.; RT "A method for determining the position and size of optimal RT sequence regions for phylogenetic analysis."; RL J. Mol. Evol. 41:1128-1138(1995). ADDRESS R&D Department, TDI ADDRESS c/ Condes de Torreanaz, 5 ADDRESS 28028, Madrid ADDRESS SPAIN CONTACT martin@tdi.es CONTACT dopazo@tdi.es SITE ftp anonymous ftp.tdi.es SITE Directory /pub/programas/ SITE-CONTACT martin@tdi.es SITE WWW Server at URL http://www.tdi.es/programas/osa-i.htm OS UNIX (Solaris, Irix) LANGUAGE GPC Pascal VOLUME 300K REQUIRES GPC for compiling sources COMMENTS OSA is available as both : executable file for Solaris or COMMENTS Irix operating systems and sources files. GPC compiler is COMMENTS only necessary if you download the sources. AC BC00515 NAME DROSOPOSON DOMAIN Genetic tools DOMAIN Population Genetics DOMAIN Database and analysis DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION An object-oriented knowledge base dedicated DESCRIPTION on localisation data of transposable element insertions DESCRIPTION along the polytene chromosomes of Drosophila. The base DESCRIPTION brings together: DESCRIPTION 1) data available on chromosomal localisations of DESCRIPTION transposable element insertions and on features of the DESCRIPTION polytene chromosomes (DNA content, recombination rate, DESCRIPTION breakpoints...), 2) some statistical methods aimed at DESCRIPTION analysing the distribution of the transposable element DESCRIPTION insertions along the chromosomes, in relation with the DESCRIPTION chromosome features. DROSOPOSON can thus be used either as DESCRIPTION a consultation tool, as an instant look of the available DESCRIPTION knowledge, or to analyse user's data. AUTHOR Christine HOOGLAND RA Hoogland C., Biemont C.; RT "DROSOPOSON: a knowledge base on chromosomal localization of RT transposable element insertions in Drosophila."; RL Compu. Appl. Biosci. 13:61-68(1997). ADDRESS Laboratoire de Biometrie, Genetique et Biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne ADDRESS France CONTACT hoogland@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/drosoposon SITE-CONTACT - OS Sun/Solaris LANGUAGE LE_LISP VOLUME - REQUIRES - COMMENTS Commercial softwares needed: Le_Lisp and Aida by ILOG (ILOG SA, Gentilly, France); COMMENTS Knowledge base manager: SHIRKA developed by INRIA and the ARTEMIS laboratory in Grenoble, COMMENTS France (Francois.Rechenmann@inria.fr). COMMENTS All the files (data, programs, schemes) are available independently, as plain text. AC BC00527 NAME tRNAscan-SE DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN WWW server DOMAIN Statistical significance SERVER http://genome.wustl.edu/eddy/tRNAscan-SE/ DESCRIPTION tRNAscan-SE identifies transfer RNA genes in genomic DNA or DESCRIPTION RNA sequences. It combines the specificity of the Cove DESCRIPTION probabilistic RNA prediction package (Eddy & Durbin, 1994) DESCRIPTION with the speed and sensitivity of tRNAscan 1.3 (Fichant & DESCRIPTION Burks, 1991) plus an implementation of an algorithm described DESCRIPTION by Pavesi and colleagues (1994) which searches for DESCRIPTION eukaryotic pol III tRNA promoters. tRNAscan-SE identifies DESCRIPTION 99-100% of transfer RNA genes in DNA sequence while giving DESCRIPTION less than one false positive per 15 gigabases. The program DESCRIPTION searches at approximately 30,000 bp per second. Other DESCRIPTION features include prediction of tRNA secondary structure, DESCRIPTION and detection of unusual tRNA homologues such as DESCRIPTION selenocysteine tRNAs, tRNA-derived repetitive elements and DESCRIPTION tRNA pseudogenes. AUTHOR Todd M. Lowe, Sean R. Eddy RA Lowe T.M., Eddy S.R.; RT "tRNAscan-SE: a program for improved detection RT of transfer RNA genes in genomic sequence."; RL Nucleic Acids Res 25: 955-964 (1997). RA Eddy, S.R., Durbin, R.; RT "RNA Sequence Analysis Using Covariance Models"; RL Nucleic Acids Res. 22: 2079-2088 (1994). RA Fichant G.A., Burks C.; RT "Identifying potential tRNA genes in genomic RT DNA sequences"; RL J Mol Biol 220: 659-671 (1991). RA Pavesi A., Conterio F., Bolchi A., Dieci G., RA Ottonello S.; RT "Identification of new eukaryotic tRNA genes in RT genomic databases by a multistep weight matrix RT analysis of transcriptional control regions."; RL Nucleic Acids Res. 22:1247-1256 (1994). ADDRESS Dept. of Genetics ADDRESS Washington University School of Medicine ADDRESS 660 S. Euclid, Box 8232 ADDRESS St. Louis MO 63110 CONTACT lowe@genetics.wustl.edu SITE WWW Server at URL http://genome.wustl.edu/eddy/tRNAscan-SE/ OS UNIX LANGUAGE C, Perl VOLUME - REQUIRES Perl 5.0+ AC BC00529 NAME The USC Sequence Alignment Package DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment Search software DOMAIN Statistical significance DOMAIN WWW server SERVER http://www-hto.usc.edu/software/seqaln/ DESCRIPTION This library of functions aligns nucleotide and DESCRIPTION protein sequences finding global, local, overlapping, DESCRIPTION and fitting regions of alignment using the generalized DESCRIPTION Smith-Waterman linear gap function g(k) = DESCRIPTION a + b(k-1) with one or two DNA, RNA or one-letter coded protein sequences. Also finds DESCRIPTION statistical significance of local alignments using the Poisson clumping heuristic. DESCRIPTION DESCRIPTION The package also includes GFSR, a good pseudorandom number generator, and standalone DESCRIPTION programs to perform global, local, fit and overlap alignments. AUTHOR Paul Hardy, Michael S. Waterman RT - ADDRESS Department of Mathematics ADDRESS University of Southern California ADDRESS 1042 W. 36th Place, DRB 155 ADDRESS Los Angeles, CA 90089-1113 CONTACT phardy@hto.usc.edu SITE WWW Server at URL http://www-hto.usc.edu/software/seqaln/ OS - LANGUAGE C VOLUME - REQUIRES - AC BC00560 NAME Alkami Expert for PCR DOMAIN Sequence analysis DOMAIN Genetic tools DOMAIN WWW server DOMAIN Statistical significance SERVER http://www.alkami.com DESCRIPTION A PCR (polymerase chain reaction)design, troubleshooting and DESCRIPTION optimization tool. Alkami PCR integrates PCR reference DESCRIPTION resources and statistical tools with a simple interface. AUTHOR - RT - ADDRESS Alkami Biosystems ADDRESS P.O. Box 11216 ADDRESS Berkeley, CA 94712-2216 CONTACT info@alkami.com SITE WWW Server at URL http://www.alkami.com OS - LANGUAGE - VOLUME - REQUIRES - COMMENTS This is a FREE online service intended to introduce COMMENTS molecular biologists to a powerful PCR optimization tool. AC BC00570 NAME RASA 2.2 DOMAIN Sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION RASA 2.2 provides a set of tools for measuring DESCRIPTION phylogenetic signal and for studying its distribution DESCRIPTION among taxa. DESCRIPTION DESCRIPTION This software is used for DESCRIPTION * measuring signal DESCRIPTION * testing the suitability of available outgroup taxa DESCRIPTION * detecting long branches in the taxon variance plot DESCRIPTION * performing the mixed-character taxon test for differential DESCRIPTION lineage sorting DESCRIPTION * performing bootstrap power and effect to examine the DESCRIPTION power curve for your data. DESCRIPTION DESCRIPTION Exploratory options include DESCRIPTION * determining the signal spectrum for a set of sequences DESCRIPTION * removing noisy sites DESCRIPTION DESCRIPTION Some researchers have used the software to examine DESCRIPTION hypotheses of alignment using phylogenetic signal as the DESCRIPTION criterion. DESCRIPTION DESCRIPTION This software can be used on discrete data (molecular, DESCRIPTION morphological, or mixed). AUTHOR James Lyons-Weiler, PhD RA Lyons-Weiler, J., Hoelzer, G.A. and Tausch R.J.; RT "Relative Apparent Synapomorphy Analysis (RASA) I: RT the statistical measurement of phylogenetic signal."; RL Molecular Biology and Evolution 13:749-757(1996). RA Lyons-Weiler, J. and Milinkovitch, M.C.; RT "A phylogenetic approach to the problem of differential RT lineage sorting."; RL Molecular Biology and Evolution 14:968-975(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RT "Escaping from the Felsenstein Zone by detecting long RT branches in phylogenetic data."; RL Molecular Phylogenetics and Evolution 8:375-384(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RL "Optimal outgroup analysis."; RL Biological Journal of the Linnean Society 64:493(1998). RA Milinkovitch, M.C. and Lyons-Weiler, J.; RT "Finding optimal outgroup topologies and convexities RT when the choice of outgroups is not obvious."; RL Molecular Phylogenetics and Evolution 9:348-357(1998). ADDRESS - CONTACT jfl8@psu.edu SITE WWW Server at URL http://test1.bio.psu.edu/LW/list.htm OS Mac/PowerPC REQUIRES All superfluous extensions off. COMMENTS The software will be updated and bugs fixed at COMMENTS irregular intervals. Watch for updates. AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00596 NAME SimPlot DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Molecular Evolution DOMAIN Statistical significance DESCRIPTION SimPlot is a graphical program for analysis of sequences DESCRIPTION (e.g. HIV) suspected of being recombinant. The program DESCRIPTION recognizes multiple file formats, and sequences can be DESCRIPTION analyzed individually or as members of groups. Three DESCRIPTION major methods are available: similarity/diversity plots, DESCRIPTION bootscanning, and informative site analysis. Results DESCRIPTION can be printed, copied to the Windows clipboard, or DESCRIPTION saved as a graphics metafile. The author reserves DESCRIPTION copyright, but the software is provided at no cost. AUTHOR Stuart C. Ray, M.D. RA Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., RA Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., and Ray S.C.; RT "Full-Length Human Immunodeficiency Virus Type 1 Genomes RT from Subtype C-Infected Seroconverters in India, with RT Evidence of Intersubtype Recombination"; RL J Virol 73:152-160 (1999). ADDRESS Stuart C. Ray, M.D. ADDRESS Division of Infectious Diseases ADDRESS Johns Hopkins University School of Medicine ADDRESS 720 Rutland Avenue, Ross 1159 ADDRESS Baltimore, MD 21205 CONTACT sray@jhmi.edu SITE WWW Server at URL http://www.med.jhu.edu/deptmed/sray/download/ OS Windows 95, Windows 98, Windows NT LANGUAGE Pascal (Borland Delphi) VOLUME 1.2 MB REQUIRES 32-bit PHYLIP (phylip95.exe)