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.
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.
Software, UK. Alice Biodiversity Data Management
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
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
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.
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.
Botanical Garden Database, USA. BG-BASE is a
botanical collections management database in use in
botanical gardens and arboreta worldwide.
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.
Biologische Kartierungen, von Stefan Wehr, Offenbach,
Germany. Eine vorläufige Information vom Autor des
Education Software FAQ by Eli Meir and the Biology
Education Software Taskforce of the University of
Newsgroup Archive. Searchable archives of this
-- Software for Computing Plant Biomass
- 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
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.
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.
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
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.
Documentation (Collection And Specimen System for
Information and Analysis), New York Botanical Garden,
Studies for Monitoring Programs, Power Analysis, Patuxent
Wildlife Research Center, Biological Resources Division,
U.S. Geological Survey
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
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
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.
programs for pollen analysis from Cambridge
Plant Evolution and Palaeoecology, UK.
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.
TWINSPAN and TABLCORN DOS programs written by Mark
Hill, Institute of
Terrestrial Ecology, Monks Wood, Abbots Ripton,
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.
- 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.
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.
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
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"
Software. A British site with ecological software
rangeing from growth analysis to diversity programs.
(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.
Software: Scientific software for teaching and research.
A company selling software for statistics, ecology,
genetics, data acquisition, identification, and other.
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
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.
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.
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,
- 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.
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
5 (software for vegetation analysis), Robert
Wiedermann, Angew.Stat&EDV, Boku Wien, Austria.
(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.
Data-Handling File Boutique (Louis J. Maher, Wisconsin,
- 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)
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.
- Dichotomous Key Software
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,
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.
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
- 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.
Wildlife recording and collection management software for
the Macintosh. Shareware, $50.
a WWW online multivariate analysis system set up by Jean
Thiolouse, Laboratory of Biometry, University of Lyon,
Methods for Ecologists by Michael Palmer, Oklahoma State
- 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.
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
Analysis Software. Cladistics software from the
International Willi Hennig Society, USA.
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
an application for phylogenetic tree drawing
Analysis Computer Programs from the Tree of Life
site, Arizona, USA.
software - Nascent software for the Mac by James
Lyons-Weiler at University of Nevada, USA
Software Resources, a list from the Museum of
Paleontology, University of California at Berkeley.
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.
- 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
Plants in Britain and Ireland on CD-ROM, Royal
Botanic Gardens Kew, UK.
(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.
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
software from the Swedish Agricultural University (SLU).
DOS programs for scientific reference management, spatial
point analysis, taxonomy (TAXOKEY etc.), experimental
design and sampling etc.
v5.6 for Biodiversity Data Capture, Checklisting and
Communications via ftp from Vaasa, Finland.
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.
for Pest Management, CRC for Tropical Pest
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
System for Easy Analysis of Lots of Sequences (SEALS).
SEALS is a free software package expressly designed for
large-scale research projects in bioinformatics.
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.
and Nomenclature Software, a list from BIOSIS
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.
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).
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.
Taxonomy and Systematics at Glasgow, UK. TreeView is a
free, simple program for displaying phylogenies on Apple
Macintosh and Windows Pcs.
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.
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.
USA. Webcutter is a free on-line tool for restriction
mapping nucleotide sequences. - Mirror of
WebCutter in Gothenburg, Sweden.
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
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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)