Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00265 NAME BH - MBCRR DOMAIN Sequence format conversion tools DESCRIPTION MBCRR Software Package DESCRIPTION Converts IntelliGenetics-formatted sequence DESCRIPTION files into hash files (the required input DESCRIPTION file type for DASHER). AUTHOR - RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00266 NAME CONVERSION DOMAIN Sequence format conversion tools DESCRIPTION Conversion programs DESCRIPTION GenBank to IG gbtoig DESCRIPTION EMBL/SWISS-PROT to IG embltoig DESCRIPTION FASTA to IG fastatoig DESCRIPTION GenBank to FASTA gbtofasta DESCRIPTION EMBL/SWISS-PROT to FASTA embltofasta DESCRIPTION IG to FASTA igtofasta AUTHOR Spencer Yeh RT - ADDRESS - CONTACT - SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00268 NAME DBCONV DOMAIN Sequence format conversion tools DESCRIPTION Transformation of line-oriented databases into DESCRIPTION tab-delimited format AUTHOR Valverde J.R. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Vax/VMS LANGUAGE C VOLUME - AC BC00269 NAME EMBL2NBRF DOMAIN Sequence format conversion tools DESCRIPTION Create NBRF-style primary data base files from EMBL flat file. DESCRIPTION GCG-styled splitting of sequences longer than 350,000 is done. AUTHOR Jack A.M. Leunissen RT - CONTACT jackl@caos.kun.nl ADDRESS CAOS/CAMM Center University of Nijmegen ADDRESS Toernooiveld 1,6525 ED Nijmegen The Netherlands SITE ftp anonymous ftp.caos.kun.nl SITE Directory /pub/molbio/embl2nbrf SITE-CONTACT ackl@caos.kun.nl SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix SITE-CONTACT nethelp@ebi.ac.uk OS Unix , VMS LANGUAGE C VOLUME - AC BC00270 NAME FROMGB DOMAIN Sequence format conversion tools DESCRIPTION convert from GenBank LOCUS format (also DESCRIPTION used by the IBI-Pustell programs) to Pearson/ DESCRIPTION FASTA format. AUTHOR William R. Pearson RT - ADDRESS U. of Virginia Dept. of Biochemistry, USA CONTACT William R. Pearson wrp@virginia.edu 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 BC00271 NAME GB2FASTA DOMAIN Sequence format conversion tools DESCRIPTION It is part of the blast package DESCRIPTION produce a file in FASTA format from one in DESCRIPTION GenBank(R) flat file format. AUTHOR - RT - ADDRESS - CONTACT - SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /pub/blast SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00272 NAME GT2FASTA DOMAIN Sequence format conversion tools DESCRIPTION Basic Local Alignment Search Tool (blast package) DESCRIPTION family of sequence database comparison programs DESCRIPTION produce a file in FASTA format from the CDS DESCRIPTION (coding sequence)features in a GenBank(R) flat DESCRIPTION file. AUTHOR - RT - CONTACT - SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00273 NAME N2A DOMAIN Sequence format conversion tools DESCRIPTION N2A is a unix filter that translates nucleic acid sequences DESCRIPTION to amino acid sequences. AUTHOR - RT - ADDRESS - CONTACT - SITE ftp anonymous grog.mbb.sfu.ca SITE Directory /pub/n2a SITE-CONTACT - OS Unix (SunOS, Ultrix,SGI), LINUX LANGUAGE - VOLUME - REQUIRES - AC BC00274 NAME PDBTOGCG DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Extracts protein squences from PDB files AUTHOR Mezei M. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS VAX/VMS LANGUAGE FORTRAN VOLUME - AC BC00275 NAME PIR2FASTA DOMAIN Sequence format conversion tools DESCRIPTION Basic Local Alignment Search Tool DESCRIPTION family of sequence database comparison DESCRIPTION programs produce a file in FASTA format from DESCRIPTION one in NBRF PIR(R) format. AUTHOR - RT - ADDRESS - CONTACT - SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - AC BC00276 NAME PROSITEC DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Conversion of Prosite database to GCG Find DESCRIPTION format AUTHOR Hofmann K. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS VAX/VMS LANGUAGE Pascal VOLUME - AC BC00277 NAME PRSEQ DOMAIN Sequence format conversion tools DESCRIPTION MBCRR Software Package DESCRIPTION Formats and prints sequences. AUTHOR - RT - ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00278 NAME READSEQ DOMAIN Sequence format conversion tools DESCRIPTION Sequence format conversion tools AUTHOR Gilbert D. (mods by Alff-Steinberger A.) RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE-CONTACT nethelp@ebi.ac.uk SITE gopher Host: ftp.bio.indiana.edu Port: 70 SITE URL gopher://ftp.bio.indiana.edu:70/11/IUBio-Software+Data/molbio/readseq SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/readseq SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix Vax/VMS LANGUAGE C VOLUME - COMMENTS This program may be freely copied and used by COMMENTS anyone AC BC00279 NAME SEQCNV DOMAIN Sequence format conversion tools DESCRIPTION MBCRR Software Package DESCRIPTION Converts non-standard formatted sequences DESCRIPTION into IntelliGenetics file format (the DESCRIPTION sequence format used by most MBCRR software). AUTHOR WW Ralph, T Webster, TF Smith, RA Ralph W.W., Webster T., Smith T.F.; RT "A modified Chou and Fasman protein structure algorithm."; RL Comput. Appl. Biosci. 3:211-216(1987). RX Medline; 88270157. RX SeqAnalRef; RALW8701. ADDRESS Molecular Biology Computer Research Resource ADDRESS Dana-Farber Cancer Institute and School of Public Health ADDRESS Harvard University, 44 Binney St., Boston MA 02115 USA. CONTACT Smith T: tsmith@mbcrr.harvard.edu SITE ftp anonymous mbcrr.harvard.edu SITE Directory /MBCRR-Package SITE-CONTACT Smith T: tsmith@mbcrr.harvard.edu OS Unix LANGUAGE C VOLUME - AC BC00280 NAME TDF2GCG DOMAIN Sequence format conversion tools DOMAIN GCG tools DESCRIPTION Program to convert the SITES table of the TFD DESCRIPTION database to GCG format. AUTHOR Mathog D. RT - ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk OS Vax/VMS LANGUAGE FORTRAN C VOLUME - REQUIRES GCG package AC BC00281 NAME TDF2PROSITE DOMAIN Sequence format conversion tools DESCRIPTION Program to convert SITES and DOMAINS tables of DESCRIPTION TFD database to Prosite format. AUTHOR Fuchs R. RT - ADDRESS Glaxo Research Institute, 5 Moore Drive, Research Triangle Park, ADDRESS NC 27709, USA CONTACT rf11522@glaxo.com SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE C 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 BC00427 NAME DataMinder DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Oligomer design and synthesis DOMAIN Database and analysis DESCRIPTION DataMinder is a standalone data management program designed DESCRIPTION for molecular biologists. One can readily store and retrieve DESCRIPTION data about oligonucleotides, nucleic acid or protein DESCRIPTION sequences, recombinant DNA clones, cells, reagents and DESCRIPTION protocols .A number of utilities for data analysis are provided, DESCRIPTION including those for calculating the Tms of oligonucleotides and DESCRIPTION for the evaluation of oligonucleotides for use as DESCRIPTION hybridization probes or primers for DNA synthesis. A DESCRIPTION variety of sequence editing features including voice veri- DESCRIPTION fication and the ability to import and export sequence data DESCRIPTION in a variety of different formats are also provided.Context- DESCRIPTION sensitive help is provided. DataMinder is simple to use and to DESCRIPTION customize and allows for sharing of database information DESCRIPTION across a computer network. AUTHOR Karen Usdin RA Usdin K.; RT "Hypercard-based data management tools for molecular biologists."; RL Comput. Appl. Biosci. 8:107-111(1992). RX Medline; 92274208. RX SeqAnalRef; USDK9201. ADDRESS Building 8, Room 202 ADDRESS 8 Center DR MSC 0830 ADDRESS National Institutes of Health ADDRESS Bethesda, MD 20892-0830 ADDRESS U.S.A. CONTACT ku@helix.nih.gov SITE - SITE-CONTACT - OS MAC LANGUAGE C, hypertalk VOLUME - REQUIRES Mac SE or above, 2MB Ram AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00470 NAME Primer Premier 4 DOMAIN Oligomer design and synthesis DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN RNA analysis DOMAIN Restriction maps DESCRIPTION Primer Design Software DESCRIPTION Primer Premier 4 is now available for Power Macintosh and DESCRIPTION Window 3.1, NT as well as Windows 95. Primers can be DESCRIPTION designed for PCR, sequencing or hybridization probes DESCRIPTION automatically or with full manual control. DESCRIPTION From the selected pool of primers mutually compatible DESCRIPTION Nested/Multiplex primers or pairs can be chosen. DESCRIPTION Any primer can be mutated using the editing facility. DESCRIPTION Full degeneracy is supported. Comprehensive analyis of DESCRIPTION secondary structures as well as a table of properties DESCRIPTION including melting temperature calculated using nearest DESCRIPTION neighbor theory and optimal annealing temperature is DESCRIPTION displayed for each primer. DESCRIPTION DESCRIPTION The selected primers can be managed with the database DESCRIPTION storage facility. The program even makes the primer DESCRIPTION synthesis process painless by automatically creating an DESCRIPTION order form addressed to the vendor of your choice. DESCRIPTION DESCRIPTION Restriction enzyme analysis is available with multiple DESCRIPTION output formats: table, annotated sequence or map. Functions DESCRIPTION to edit the sequence and to translate it using standard or DESCRIPTION any mitochondrial/organelle codon table is provided. Graphs DESCRIPTION of melting temperature, internal stability and free energy DESCRIPTION are available on-line as well as in printed format. AUTHOR Premier Biosoft International RT - ADDRESS 3786 Corina Way ADDRESS Palo Alto, CA 94303 CONTACT sales@PremierBiosoft.com SITE WWW Server at URL http://www.PremierBiosoft.com OS Windows 95, 98, NT, 3.1, Power Macintosh LANGUAGE - VOLUME - REQUIRES - COMMENTS Commercial product, fully functional demo available at COMMENTS http://www.PremierBiosoft.com page. AC BC00476 NAME SEQIO DOMAIN Sequence format conversion tools DESCRIPTION SEQIO is a C/C++ package for reading and writing sequences in DESCRIPTION a number of different formats, including GenBank, EMBL, PIR, DESCRIPTION FASTA, IG/Stanford, Clustal, PHYLIP and others. It is available DESCRIPTION for Unix and Windows NT/95 systems. DESCRIPTION Including in the distribution is a file format conversion program, DESCRIPTION fmtseq, which is a reimplementation and extension of Don Gilbert's DESCRIPTION readseq program, and a fixed-width motif searching program. AUTHOR Knight, James RT - ADDRESS Dept. of Computer Science ADDRESS Univ. of California, Davis ADDRESS Davis CA 95616 CONTACT knight@cs.ucdavis.edu (James Knight) SITE ftp anonymous ftp.cs.ucdavis.edu SITE Directory /pub/strings/seqio.tar.gz SITE-CONTACT knight@cs.ucdavis.edu SITE WWW Server at URL http://wwwcsif.cs.ucdavis.edu/~knight/seqio.html OS Unix, Windows NT LANGUAGE C, C++ VOLUME - REQUIRES An ANSI C or C++ compiler COMMENTS Complete documentation is available on the WWW server AC BC00497 NAME Sequin DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Sequence data submissions DESCRIPTION Sequin is a stand-alone software tool developed by the NCBI DESCRIPTION for submitting entries to the GenBank, EMBL, or DDBJ DESCRIPTION sequence databases. It is capable of handling simple DESCRIPTION submissions which contain a single short mRNA sequence, and DESCRIPTION complex submissions containing long sequences, multiple DESCRIPTION annotations, segmented sets of DNA, or phylogenetic and DESCRIPTION population studies. AUTHOR Jonathan Kans, Colombe Chappey RT - ADDRESS NIH/NLM/NCBI ADDRESS Building 38A, Room 8N805 ADDRESS Bethesda, MD 20894 ADDRESS U.S.A. CONTACT info@ncbi.nlm.nih.gov SITE ftp anonymous ncbi.nlm.nih.gov SITE Directory /sequin SITE-CONTACT info@ncbi.nlm.nih.gov SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Sequin OS Mac (68K and PPC), Windows (16 and 32 bit), Unix (Sun, Solaris, SGI, Linux, DEC) LANGUAGE English VOLUME - REQUIRES - COMMENTS Information about this package is available from COMMENTS http://www.ncbi.nlm.nih.gov/Sequin AC BC00500 NAME DnaSP DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Population Genetics DESCRIPTION DnaSP is a software package for Windows that DESCRIPTION performs extensive population genetics analyses on DNA DESCRIPTION sequence data. DESCRIPTION DnaSP estimates several measures of DNA sequence DESCRIPTION polymorphism within and between populations (in noncoding, DESCRIPTION synonymous or nonsynonymous sites), linkage disequilibrium, DESCRIPTION recombination, gene flow, and gene conversion. DESCRIPTION The program can also perform the analysis of the pairwise DESCRIPTION differences distribution (mismatch distribution), and the DESCRIPTION frequency spectrum in constant size and in growing populations. DESCRIPTION DnaSP can also conduct some neutrality tests: Fu and DESCRIPTION Li's; Hudson, Kreitman and Aguade; McDonald and Kreitman; DESCRIPTION and Tajima's tests. DESCRIPTION DnaSP can estimate the confidence intervals of some test- DESCRIPTION statistics by the coalescent. DESCRIPTION DnaSP allows performing several analyses by the sliding window DESCRIPTION method, and also to obtain graphic representations. DESCRIPTION Input: Aligned DNA sequences in NBRF/PIR, MEGA, PHYLIP and NEXUS DESCRIPTION file formats. DESCRIPTION Output: the results are displayed in tables and graphs. The DESCRIPTION output can be either sent to the printer or saved in a file. DESCRIPTION The program can handle a large number of sequences (hundreds) DESCRIPTION of thousands of nucleotides each. AUTHOR Julio Rozas and Ricardo Rozas RT "DnaSP version 3: an integrated program for molecular population RT genetics and molecular evolution analysis" RL Bioinformatics 15: 174-175 (1999). ADDRESS Departament de Genetica ADDRESS Facultat de Biologia ADDRESS Universitat de Barcelona ADDRESS Diagonal 645 ADDRESS Barcelona 08071 ADDRESS Spain ADDRESS Phone: +34 93-4021495 ADDRESS Fax: +34 93-4110969 CONTACT julio@porthos.bio.ub.es SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/dnasp SITE-CONTACT nethelp@ebi.ac.uk SITE DnaSP updates: SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html OS Winodws 95, 98, NT LANGUAGE Visual Basic 5.0 VOLUME 3992 Kb REQUIRES PC Pentium, 16 Mb RAM COMMENTS For academic uses, DnaSP is available free of charge AC BC00520 NAME Miropeats DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Alignment Search software DOMAIN Alignment editing and display DESCRIPTION Miropeats is a graphical DNA sequence comparison tool. DESCRIPTION It can be used in almost all situations where one would DESCRIPTION normally use sequence alignments or dot plots to compare DESCRIPTION DNA sequences. However, Miropeats improves on dotplots DESCRIPTION in two ways, firstly, by allowing multiple sequences to DESCRIPTION be compared simultaneously and, secondly, by usually DESCRIPTION presenting a realtively intuitive graphic. It improves DESCRIPTION on large alignments by summarising all the similarities DESCRIPTION on a single page of PostScript (TM) graphics. AUTHOR Jeremy Parsons RA Parsons J.D.; RT "Miropeats: graphical DNA sequence comparisons."; RL Comput. Appl. Biosci. 11(6):615-619(1995). RA Parsons J.D.; RT "Improved tools for DNA comparison and clustering."; RL Comput. Appl. Biosci. 11(6):603-613(1995). ADDRESS European Bioinformatics Institute, ADDRESS Wellcome Trust Genome Campus, ADDRESS Hinxton, ADDRESS Cambridge ADDRESS CB10 1SD ADDRESS England CONTACT Jeremy.Parsons@ebi.ac.uk SITE WWW Server at URL http://genome.wustl.edu/est/esthmpg.html OS Solaris, IRIX, OSF, UNIX LANGUAGE C-shell, ANSI-C VOLUME - REQUIRES PostScript printing or viewing AC BC00564 NAME SEALS: A System for Easy Analysis of Lots of Sequences DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION SEALS (A System for Easy Analysis of Lots of Sequences) is a DESCRIPTION free, public domain package for large-scale sequence analysis DESCRIPTION investigations. It is still under development, but already DESCRIPTION provides a number of very useful programs, including unique DESCRIPTION taxonomy-aware tools. AUTHOR Walker DR, Koonin EV RA Walker DR, Koonin EV; RT "SEALS: A System for Easy Analysis of Lots of Sequences"; RL ISMB 5:333-339(1997). ADDRESS D Roland Walker ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1 (301)435-5909 Fax: +1 (301)435-5909 ADDRESS email: walker@ncbi.nlm.nih.gov ADDRESS ADDRESS Eugene V. Koonin, PhD ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1(301)435-5913 Fax:+1 (301)480-9241 ADDRESS email: koonin@ncbi.nlm.nih.gov CONTACT walker@ncbi.nlm.nih.gov (Roland Walker) SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html OS Unix LANGUAGE Perl VOLUME 150 MB REQUIRES a number of other programs and db detailed on the home page AC BC00587 NAME BioEdit DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN RNA analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Searching databases DOMAIN General tools DESCRIPTION BioEdit is a user-friendly, graphically-oriented sequence DESCRIPTION alignment editor for Windows 95/98/NT. Features include DESCRIPTION several modes of hand alignment, auto-linking to ClustalW, DESCRIPTION user-defined color view (editable by mouse point- and DESCRIPTION click), separate amino acid and nucleotide color tables, DESCRIPTION Shaded views with many options, RNA comparative analysis DESCRIPTION tools (including mutual information with interactive 2-D DESCRIPTION matrix plots and area plots), restriction mapping, browsing DESCRIPTION restriction enzymes by company, easy plasmid drawing and DESCRIPTION annotation, protein hydropathy plots, can handle very large DESCRIPTION alignments (up to 20000 sequences of undefined length), DESCRIPTION several translation modes, nucleotide/translation toggling DESCRIPTION for alignment in both protein and DNA views, 6-frame DESCRIPTION translations, basic sequence manipulations (complement, DESCRIPTION reverse, uppercase, lowercase), internal web browser (HTML DESCRIPTION 2.0-compliant), auto-link to external browser with internet DESCRIPTION bookmarks, on-line help system, configure external apps via DESCRIPTION a graphical interface to automatically run through a DESCRIPTION BioEdit interface, split-window views for editing of two DESCRIPTION different places in an alignment at the same time, local DESCRIPTION NCBI BLAST accessories, single sequence editing and DESCRIPTION manipulation, retains GenBank data (eg, FEATURES, DESCRIPTION REFERENCE, SOURCE, PID or NID, etc), binary file format for DESCRIPTION fast save/open of very large files (alignments up to 100 Mb DESCRIPTION and more are no problem), correct spacing of all available DESCRIPTION fonts in edit window and in shaded view, creation of DESCRIPTION high-quality alignment figures via shading with many DESCRIPTION options (including full-color, id/sim shading, enhanced DESCRIPTION metafile copy and paste directly into graphics programs), DESCRIPTION easy formatted text print preview. AUTHOR Tom Hall RT - ADDRESS Department of Microbiology, ADDRESS North Carolina State University ADDRESS Raleigh, NC 27695 CONTACT tahall2@unity.ncsu.edu SITE WWW Server at URL http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html OS Windows LANGUAGE - VOLUME BioEdit.zip file = 7.6 Mb REQUIRES Windows 95, 98 or NT, Pentium 60+, 16 Mb RAM+, REQUIRES 20 Mb hard drive space 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 BC00590 NAME FASTA SCAN DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN GCG tools DOMAIN Alignment editing and display DOMAIN Alignment browser DESCRIPTION FASTA SCAN allow you to select and save sequences of real DESCRIPTION interest from a FASTA output. DESCRIPTION This version was successfully tested with: DESCRIPTION - FASTA of GCG package (v.8.1 and 10) DESCRIPTION - FASTA of "Pearson package" version 3.1t07 May, 1998 DESCRIPTION The maximum number of sequences is 1000. AUTHOR Olivier Friard RT - ADDRESS Dipartimento di Genetica, Biologia e Biochimica ADDRESS via Santena, 5bis ADDRESS I-10126 TURIN ITALY CONTACT friard@molinette.unito.it SITE WWW Server at URL http://pcgen018.molinette.unito.it/programs.html OS win95, win98, NT 4.0 LANGUAGE - VOLUME - REQUIRES - AC BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence AC BC00595 NAME SeqVerter DOMAIN Sequence format conversion tools DESCRIPTION A free sequence format converter for MS DESCRIPTION Windows. Has drag-and-drop compatibility, includes a DESCRIPTION sequence viewer, and a function to trim low confidence DESCRIPTION regions from automatic sequencer traces. AUTHOR GeneStudio, Inc. RT - ADDRESS - CONTACT info@genestudio.com SITE WWW Server at URL http://www.genestudio.com SITE-CONTACT info@genestudio.com OS Windows 9x/NT LANGUAGE N/A VOLUME - REQUIRES -