INTERNET DIRECTORY FOR BOTANY: SOFTWARE

Original location of this page: http://www.helsinki.fi/kmus/botsoft.html

For mapping software, please visit Cartographic Links for Botanists.

• Aditsite, Microsoft Windows software for environmental assessment, wildlife recording, and species identification. Sold by Adit Limited, Anglesey, UK.
• Aldex Sofware, UK The site includes various software developed by Aldex Software, a software house specialising in landscape and horticultural software and including : Plant Selector Plant Selector Professional Garden Designer Professional LandCalc (calculates areas/volumes/ etc by tracing maps or plans) LandMate (Landscape estimating package) LandMan (Comprehensive Landscape management) and various other horticulture related software.
• Alice Software, UK. Alice Biodiversity Data Management System.
• An annotated bibliography of canonical correspondence analysis and related constrained ordination methods 1986-1993 by H. J. B. Birks, Sylvia M. Peglar and Heather A. Austin, Botanical Institute, University of Bergen, Norway.
• AX-Orion, USA. An easy to use, yet powerful WWW PC database server. It has full query / insert / update / delete functionality and supports major brand PC database systems. University of Michigan (MICH) Fungus Collection gives an example of the use of this program.
• BEnTroS data base system is designed to inquire plant species and their ability for methods in the field of biological in the tropics and subtropics.
• BG-MAP, Botanical Garden Mapping System, USA. Information on computerized mapping of plant collections typically housed at facilities such as botanical gardens, arboreta, zoos, and large private estates.
• BG-BASE Botanical Garden Database, USA. BG-BASE is a botanical collections management database in use in botanical gardens and arboreta worldwide.
• Biodiversity and WORLDMAP (Natural History Museum, London). Quantitative measures for mapping biodiversity value, rarity and endemism, combined with accountable methods for assessing priority areas for biodiversity conservation, including gap analysis. The site shows examples from different spatial scales, including preliminary maps derived from AFE data for Europe, and a free downloadable demo of the WORLDMAP software.
• BIOKART. Biologische Kartierungen, von Stefan Wehr, Offenbach, Germany. Eine vorläufige Information vom Autor des Programmes.
• Biology Education Software FAQ by Eli Meir and the Biology Education Software Taskforce of the University of Washington, USA.
• Bionet.software Newsgroup Archive. Searchable archives of this newsgroup.
• BIOPAK -- Software for Computing Plant Biomass
• BIOSIS - Software Reviews, UK. Included on this page are links to over 150 reviews of biological software packages. Each review contains the following elements: software title, including version information; author(s)' and publisher's name and contact information; description of the manual if included; publication year; an abstract containing specifications for running the software and a noncritical description of what the program is intended to do.
• BioSystematica, software for electrophoretic analysis (University of Plymouth, UK). BioSystematica specializes in the creation of computer systems for the analysis of electrophoretic gel patterns, and supplies complete systems or software only. Demonstration versions of some products may be downloaded.
• BIOTA, The Biodiversity Database Manager. Specimen-based, biological data and collections management software for individuals, institutions, and projects, created by Robert K. Colwell.
• Cactus and Succulent Computer Software - CactusBase v.2.5. A computer database package for storing records of Cacti and other succulent plants, seed raising activities, literature collection and photographs.
• CanoDraw by Petr Smilauer, Czech Republic. This program is for people working or preparing to work with ordination methods (which belong to the methods of multivariate statistical analysis), typically in field of community / population ecology. It's primary purpose was to provide users of the multivariate statistical methods of gradient analysis with a possibility to interactively explore results of these methods by displaying ordination diagrams.
• Carto Fauna-Flora. CFF is Windows mapping software for representing animals and/or plant distributions. An evaluation version can be downloaded from the CFF website (the program costs $US 130 ). Zoological Laboratory, University of Mons-Hainaut, Mons, Belgium.
• CASSIA Documentation (Collection And Specimen System for Information and Analysis), New York Botanical Garden, USA
• Case Studies for Monitoring Programs, Power Analysis, Patuxent Wildlife Research Center, Biological Resources Division, U.S. Geological Survey
• Chez Marco's Fieldwork Software Checklist by Marco Bleeker, the Netherlands. List of software products that could be of interest to biologists who do fieldwork. Ecology, statistics, mapping, taxonomy, identification, management of collections: it's all there. Short info and/or links to further information, sometimes freely downloadable programs.
• CODA: software for nature conservation planning. CODA (Conservation Options and Decisions Analysis) is a software package for IBM and compatible PCs that helps you to design networks of nature reserves or protected areas, written by Michael Bedward, New South Wales National Parks and Wildlife Service, Environmental Survey and Research Branch, Australia.
• COMPARE, from the University of Oregon, USA. Computer programs for the phylogenetic analysis of comparative data. COMPARE consists of several programs which analyze comparative or interspecific data while taking phylogenetic information into account.
• COMPARE, Computer programs for the phylogenetic analysis of comparative data, from the University of Oregon, USA. COMPARE consists of several programs which analyze comparative or interspecific data while taking phylogenetic information into account.
• Computer programs for pollen analysis from Cambridge Plant Evolution and Palaeoecology, UK.
• DECODA, Database for Ecological COmmunity DAta, Australia. DECODA is a computer program for the storage, manipulation, retrieval and analysis of the kinds of data commonly collected by ecologists for the study of the composition or structure of biological communities.
• DECORANA, TWINSPAN and TABLCORN DOS programs written by Mark Hill, Institute of Terrestrial Ecology, Monks Wood, Abbots Ripton, Huntingdon, UK.
• DELTA Software and Data. DELTA (DEscription Language for TAxonomy) is a flexible format for encoding taxonomic descriptions. The data can be used to produce interactive keys (Intkey), conventional keys and descriptions, classifications, and information-retrieval systems.
• DeltaAccess - an SQL interface to Delta files, implemented in Microsoft Access. DeltaAccess has been created by Gregor Hagedorn, Inst. f. Mikrobiologie, BBA, Berlin, Germany. The application is distributed as free software under a General Public License. It requires that Windows NT 4.0 or Windows 95 and Access 97 or Access 95 are installed on a computer with at least 16 MB RAM.
• DELTA-L, A Discussion Forum for Users of the DELTA System and Related Taxonomic Software. The Delta-L Mailing List is frequented by users of a variety of descriptive-database software, including the CSIRO-created DELTA System and associated packages, LUCID, and others. Software and data that takes advantage of any of these packages is commonly shared and debated. Subscribers are often professional taxonomists and others providing classifications of flora and fauna or making use of classifications constructed with these packages.
• The DMAP information pages, UK by Dr. Alan Morton. DMAP is a computer program which produces Distribution Maps or Coincidence Maps based on data files containing the digitized features of the areas to be mapped and also the distribution data for the species to be mapped. The data files can contain co-ordinates as Grid References (kilometres and metres) or as Latitude+Longitude (degrees and minutes). DMAP can be used as a 'stand-alone' mapping package or can be linked to a general database or biological recording package which generates some or all of the required data files.
• Digital Taxonomy Web Site by Mauro J. Cavalcanti. Digital Taxonomy is an attempt to present a wide-ranging resource of information for biodiversity data management in the World Wide Web, and promote the effective use of computers for handling biological sofware development projects. Digital Taxonomy provides a range of links on software, hardware, methodologies, standards, data sources, and projects related to biodiversity data management, with emphasis on the exchange of free scientific software tools, computer techniques, and Internet addresses with links to other sources of information.
• The Echo Project. Echo is a simulation tool developed to investigate mechanisms which regulate diversity and information-processing in systems comprised of many interacting adaptive agents, or complex adaptive systems (CAS). Echo agents interact via combat, mating and trade to develop strategies for ensuring survival in resource-limited environments. Individual genotypes are encodings of rules for interactions. In a typical simulation, populations of these genomes evolve complicated networks of interactions and resource flows. Resulting networks may be thought of as resembling species communities in ecological systems. Flexibly defined parameters and initial conditions enable researchers to conduct a range of "what-if" experiments.
• Ecological Software. A British site with ecological software rangeing from growth analysis to diversity programs.
• EGID (Evaluation et Gestion Informatique de la Diversité génétique) or Computerized Management for Evaluating the Genetic Diversity, was developed at the SRA INRA-CIRAD, San Giuliano (Corse, France) for storing basic information on botanical and pomological traits of Citrus collection comprising 1160 accessions of scion varieties, rootstocks and Citrus relatives.
• Exeter Software: Scientific software for teaching and research. A company selling software for statistics, ecology, genetics, data acquisition, identification, and other.
• Fieldwork Software Checklist by Marco Bleeker, the Netherlands.
• FLORIN Information System Home Page, Russia. FLORIN is designed to deal with a wide range of data about plants: taxonomy and nomenclature, geographic distribution, herbarium and living collections, bibliographic data, etc. There is a personal MS-DOS version and a multiuser version for Unix. FLORIN supprots data entry and modification, query-by-example templates, configurable reports, data browsing, loading and importing data, GIS interface for geographic data, automated generation of labels for collections, collection management, data protection and authorization, Internet access, etc. - FLORIN Databases On-line.
• Garden and Botany Software Page by Laurence Hatch. Sources for botanical and gardening software on diskette or CD media. The site is sponsored by the International Phytocomputing Society, a professional organization of software authors, developers, historians, and users.
• GRAFICA NATURA by Steffen Hauser, Germany. GRAFICA NATURA is a realtime rendering system for visualisation of natural phenomena e.g. plant growth. A plant species can be specified by a number of botanicaly correct parameters. With these parameters the plant is grown inside the computer and can be seen at different development levels.
• Grow'Em Gardening Shareware Page. GROW'EM v4.0 - well-illustrated plant-growing software: grow plants from seed, cuttings, etc. 300-some species, propagating techniques in depth, detailed info on growth media, composting, lighting, etc. Maintained by Paul Postuma, Canada.
• Herbage by Overmind Software, San Francisco, USA. Herbage for Windows is an application that is specifically designed for keeping track and manipulating massive amounts of botanical information. The user can add, modify, sort, search and replace, and export a subset of data to the printer as a fully-formatted illustrated report. It comes with a database of ethnobotanical information. Of the more than 2600 plant species included, each entry includes one or more of the following: common names, medicinal action, ailments the plant is used to treat, indigenous use, mail-order source, range, habitat, alkaloid and nutrient content, and public-domain illustrations.
• HICLAS, Hierarchical Classification System. HICLAS is a taxonomic database system developed at Michigan State Univesity(MSU), USA, with funding from National Science Foundation(NSF). This system consists of an intuitive mouse- based graphical user interface connected to a Sybase database server at MSU. The interface allows a user to display and browse hierarchical taxonomic information and have the capability to display lineage information as well as phylogeny of a particular taxonomic group.
• HITAB 5 (software for vegetation analysis), Robert Wiedermann, Angew.Stat&EDV, Boku Wien, Austria.
• HYWIN (hypothesizing hybrids and parents using weighted intermediacy). A program implementing a simple method for objectively screening morphological variation in study sets suspected of containing hybrids (described in Taxon 45: 647-682. 1996). This method applies to a collection of specimens in which two or more species along with some or all of their hybrids are suspected to be represented. The purpose of the method is to hypothesize which specimens might be of hybrid origin, and for each of these specimens to indicate which other two specimens resemble those that might have been its parents. HYWIN was developed by Prof. George F. Estabrook, Department of Biology, University of Michigan, and Dr. Nir L. Gil-ad and Dr. Anton A. Reznicek, University of Michigan Herbarium. A Windows and DOS versions are available for downloading, along with a sample data set, and a user's guide.
• INQUA Data-Handling File Boutique (Louis J. Maher, Wisconsin, USA)
• The Integrated Conservation Networking System (ICONS) is an information management system designed to meet the needs of non-government, rural and indigenous organizations and individuals working in developing countries. ICONS for Windows (beta) software is produced by a team of conservation and information professionals supported by the Information Management Group of IUCN - The World Conservation Union, the International Development Research Center (IDRC) and the Norwegian Agency for Development Cooperation (NORAD). ICONS is copyrighted for free educational and non-profit use.
• Integrated Resource Information Systems (I.R.I.S.), USA. I.R.I.S. is a not-for-profit organization dedicated to helping forestry, natural resource, and environmental professionals make better decisions by improving the information available to them. To this end, I.R.I.S specializes in using computer technology to manage and conserve natural resources.
• IUBio Archive: biology data and software (Indiana University, USA)
• John Cheeseman's home page at Dept of Plant Biology, University of Illinois, Urbana, USA, with a program for teaching photosynthesis. You can download a demo program - more functional program is for sale.
• Keyout - Dichotomous Key Software
• LUCID, Cooperative Research Centre for Tropical Pest Management, Australia. LucID is an interactive Windows program which lets you view and construct identification keys.
• LVB 1.0: Reconstructing evolution using parsimony and simulated annealing. available. LVB uses a simulated annealing search for parsimonious trees. The program and manual are entirely free. Created by Daniel Barker, Institute of Cell and Molecular Biology, The University of Edinburgh, UK.
• MEKA, Multiple Entry Key Algorithm, MEKA is a program enable rapid identification of biological specimens. Earlier versions of the program used a command-line interface. The version offered here is the first version developed to run under Windows. MEKA is controlled by mouse clicks; no text is entered. This approach allows very rapid access to program functions. MEKA was written by Christopher A. Meacham, Museum Informatics Project, University of California, Berkeley, USA.
• MUSE Project, University of Kansas Museum of Natural History, USA- The MUSE Project is a National Science Foundation supported effort to provide software for the curation of natural history collections. The project is housed at Cornell University, USA, and is directed by Julian Humphries.
• NaturBase. 3DTX Corporation has developed an educational tool for the natural health enthusiast. NaturBase for Windows provides the user with learning experience covering 800+ common medicinal herbs, hundreds of nutrients, and over 1400 defined medical terms. Demo is available for download.
• NATUREFILE Wildlife recording and collection management software for the Macintosh. Shareware, $50.
• NetMul, a WWW online multivariate analysis system set up by Jean Thiolouse, Laboratory of Biometry, University of Lyon, France.
• Ordination Methods for Ecologists by Michael Palmer, Oklahoma State University, USA
• The PANDORA taxonomic database system, created by Richard J. Pankhurst, UK. PANDORA is a database system for biodiversity research projects, such as floras or monographs, and is the official database used at the Royal Botanic Garden Edinburgh (RBGE) for taxonomic data sets. PANDORA can also be used for maintaining catalogues of collections such as herbarium specimens and a herbarium label printing system is included. A completely functional demonstration version of PANDORA is available by FTP, or via standard mail on three diskettes.
• PANKEY. A suite of key generation and identification programs, created by Richard J. Pankhurst, UK. PANKEY is a package of programs that provide specialised tools for problems of diagnosis or identification in biology or medicine. The programs are designed to process descriptive data that are presented in a standard format (DELTA - DEscription Language for TAxonomy) and generate output suitable for use when preparing monographs, handbooks, floras or faunas. The same data can be used in the interactive identification system also included in the package.
• Parsimony Analysis Software. Cladistics software from the International Willi Hennig Society, USA.
• PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. This Web page, being constructed by Joe Felsenstein at Department of Genetics, the University of Washington, Seattle, USA, contains information on PHYLIP and ways to transfer the executables, source code and documentation to your computer. - Phylogeny Packages by Joe Felsenstein, University of Washington, Seattle, USA. Lists and descriptions of available software.
• Phylodendron, an application for phylogenetic tree drawing
• Phylogenetic Analysis Computer Programs from the Tree of Life site, Arizona, USA.
• Phylogenetics software - Nascent software for the Mac by James Lyons-Weiler at University of Nevada, USA
• Phylogenetics Software Resources, a list from the Museum of Paleontology, University of California at Berkeley.
• Plants for Windows. Plants for Windows is a plant database manager, plant locator and printing system for Microsoft Windows, designed for the serious gardener or small nursery; Prints plant lists, labels, full commercial quality catalogues, prices (any currency), price codes, descriptions, notes and cultivation instructions, with plant heights printed in metric or imperial measurements.
• Platypus - A Database Package for Taxonomists. Platypus is a Microsoft Windows-based program for managing taxonomic, geographic, ecological and bibliographic information. Platypus may be trialed free of charge by downloading a demo version.
• Poisonous Plants in Britain and Ireland on CD-ROM, Royal Botanic Gardens Kew, UK.
• PollyClave (a web-based multiple-entry identification key). Interactive identification server-side C++ program for accessing DELTA databases using CGI scripting. Polyclaves are identification tools that have a wide variety of applications across, and beyond, the life sciences. These keys allow identification of a specimen from a pool of possibilities. Characteristics of the specimen are identified, eliminating other candidates in the pool, until a unique identification is made. PollyClave can be used as a web interface for any DELTA-format polyclave database. A venture of the University of Toronto Department of Botany, the University of Toronto Libraries, and the Royal Ontario Museum of Ontario.
• RAMAS Library of Ecological Software, Applied Biomathematics, Setauket, New York, USA. RAMAS is a software library for building ecological models.
• RASA by Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. Free software for the Mac that will perform "Relative Apparent Synapomorphy Analysis", statistical test for the presence of phylogenetic signal (a.k.a. cladistic hierarchy) in _any_ type of discrete character data matrix (morphological/molecular/combined).
• Scientific software from the Swedish Agricultural University (SLU). DOS programs for scientific reference management, spatial point analysis, taxonomy (TAXOKEY etc.), experimental design and sampling etc.
• Skis v5.6 for Biodiversity Data Capture, Checklisting and Communications via ftp from Vaasa, Finland.
• SMASCH Data Entry Software and Database Structures. The Museum Informatics Project, working with the SMASCH project, is making available SMASCH database structures and data entry software for general distribution.
• Software for Pest Management, CRC for Tropical Pest Management, Australia.
• SYN-TAX multivariate data analysis program by J. Podani, Hungary. Software package for PC and Mac by János Podani, Department of Plant Taxonomy and Ecology, Eötvös University, Budapest, Hungary. Free demo version available.
• A System for Easy Analysis of Lots of Sequences (SEALS). SEALS is a free software package expressly designed for large-scale research projects in bioinformatics. 
• TAXASOFT by Eric Gouda, the Netherlands. TAXASOFT is a DELTA Data Entry/Maintenance shareware program, which makes it easy to setup and maintain your DELTA files.
• Taxonomy and Nomenclature Software, a list from BIOSIS
• Tracy, a system for the management of herbarium collections by by M. David Minnigerode, Center for the Study of Digital Libraries & The Texas A&M Bioinformatics Working Group.
• TRANSLAT, Botanical Latin Translation Program. Free-ware program by Peter Bostock, Queensland Herbarium, Australia (available also from the Missouri Botanical Garden FTP server, St. Louis, USA).
• TreeMap, Taxonomy and Systematics at Glasgow, UK. TreeMap is an experimental program for comparing host and parasite trees. It is available for both Windows and Apple Macs.
• TreeView, Taxonomy and Systematics at Glasgow, UK. TreeView is a free, simple program for displaying phylogenies on Apple Macintosh and Windows Pcs.
• TTBC, Taxonomic Tools by Computer, Museo Nacional de Ciencias Naturales, Madrid, Spain (also accessible via TTBC Gopher). Some of the services and information in the page are DIRTAX (Directory of Spanish Taxonomists; searchable by WAIS gateway) and DELTA in Spanish, and some related tools, programs for image analysis and educational purposes.
• University of California Davis Herbarium Management System. The herbarium has created a software package working in Access95. It maintains herbarium incoming and outgoing shipments; creates herbarium labels and maintains that information; maintains herbarium library (books and journals) collections; and, maintains herbarium support society (e.g. creates mailing labels; membership lists). It may be used by any non-profit institution as is.
• WebCutter, USA. Webcutter is a free on-line tool for restriction mapping nucleotide sequences. - Mirror of WebCutter in Gothenburg, Sweden.
• WINLABEL by Lanius Software (Herbarium Label-making Software). WINLABEL is a commercional, relational database program designed to maintain records of plants that you have collected for placement in an herbarium. Its primary purpose is to maintain detailed records of collected plant specimens in a format that permits you to generate one or more herbarium labels for each collected specimen. WINLABEL features an intuitive, graphical user interface and swift data entry. Print labels by county, state, location, etc. Labels are formatted to report all of your data in a clean, consistent, and professional manner; supports database entry for any state, county, or Province in North America.Customizable header and footer text; options for printing graphics.
• XID Expert System - Identification, Prescription, and Description Database Software, USA. Relational database for identification.

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This page was last updated December 11, 1998 by
Raino.Lampinen@Helsinki.Fi, Botanical Museum, Finnish Museum of Natural History (H)