About NABS

Membership application

Taxonomic certification

Classified Ads

Students & Postdocs

• Publications

Journal

Bulletin

Membership directory

NABStracts

Bibliography

• NABSLinks

Aquariums

Aquatic insects

Aquatic plants

Bibliographies

Bioassessment

Biological collections

Biological research stations

Conservation organizations

Consultants

Data and metadata directories

Ecology

Education

Equipment and Book Suppliers

GIS and Mapping

Government agencies

Hydrology

Images

Invertebrates

Job opportunities

Journals and eJournals

Just for fun

Limnology

Methods

Museums

Outreach

Phylogeny

Private research institutes

Rivers

Scientific societies

• Software

Special environments

Species list

Web indexes

Education & Outreach

Annual meeting

Journal (J-NABS)

Society Business

Members only

NABSWeb Admin

NABSLinks - Software

Email the NABS Link webmaster to suggest a new link or indicate a correction.

• ADE (550)
  (Analysis of Environmental Data) is a free multivariate analysis and graphical display package for the Macintosh.
• Biovol (380)
  BIOVOL is a DOS text-mode program for calculating the volume, surface areas, and surface to volume ratios of diatoms.
• Causal Analysis/Diagnosis Decision Information System (CADDIS) (836)
  CADDIS is an online application that helps scientists and engineers in the Regions, States and Tribes find, access, organize, use and share information to conduct causal evaluations of biological impairments in aquatic systems. It is based on the U.S. Environmental Protection Agency Stressor Identification process which is a formal method for identifying causes of impairments in aquatic systems. Current features of this site include: The Step-by-Step Guide to conducting a causal analysis; example worksheets; a library of conceptual models, and information sources including related links, glossary and acronyms, and a reference section.
• Counter 4.1 (499)
  Counter uses an IBM compatible computer as a multi-element digital laboratory counter. Keyboard keys are assigned to up to 600 user configurable items (species).Counter keeps a database of counts for these objects for up to 1000 samples that can be exported as an ASCII file and imported into almost all spreadsheet programs and statistical software. Runs in DOS to make use of the many IBM XT and 286 computers that are gathering dust in laboratories.
• Ecology Software Server at INHS (868)
  A clearinghouse for wildlife ecology related software. Subject areas include: Density Estimation, Bioacoustics, Educational, Home Range, Populations, Radio Telemetry, Habitat and General Statistics. Also include software from the the texts: Ecological Methodology (Krebs); Statistical Ecology (Ludwig and Reynolds), and Bird Flight Performance (Pennycuick).
• Eco-Tools (653)
  Eco-Tools is a web-accessible means of performing commonly-needed and useful calculations in ecology and conservation biology. Powered by webMathematica, no special software is required, and all algorithms are open-source and based on standard references. Eco-Tools is intended to be an evolving resource based on input from the ecology and conservation community. Several modules include "canned" data sets, helpful for demonstrations and teaching. Current modules include: Life Tables; Population Timeseries (Autocorrelograms and Power Spectra); Population Genetics (F-statistics); Population Viability Analysis (Simple Count-Based); Species Diversity (Species Richness); Ordination (RDA and CCA); and Taxonomic and Phylogenetic Autocorrelation (Moran's I).
• EstimateS (823)
  EstimateS 5 computes randomized species accumulation curves, statistical estimators of true species richness (S),and a statistical estimator of the true number of species shared between pairs of samples, based on species-by-sample (or sample-by-species) incidence or abundance matrices. For comparative purposes, EstimateS5 also computes Fisher's alpha and the Shannon and Simpson diversity indexes for each sample, as well as the Morisita-Horn index of biotic similarity between samples.
• G*Power (496)
  G*Power is a general power analysis program that performs high-precision statistical power analyses for the most common statistical tests ( t-tests, F-tests and Chi2-tests). The software computes: power values for given sample sizes, effect sizes, and alpha levels (post hoc power analyses); sample sizes for given effect sizes, alpha levels, and power values (a priori power analyses); and alpha and beta values for given sample sizes, effect sizes, and beta/alpha ratios (compromise power analyses). The program may be used to display graphically the relation between any two of the relevant variables and it offers the opportunity to compute the effect size measures from basic parameters defining the alternative hypothesis. [PC/DOS/Win Mac/OS9-]
• JWatcher - for the quantitative analysis of behavior (414)
  JWatcher can be used simply as an event recorder which logs the time at which keys are pressed. It was designed primarily for focal sampling, in which a single subject is observed continuously. The real power of JWatcher is, however, in its analysis routines. These calculate time budgets and provide statistics about the duration of behavioural states and the intervals between them. Version 1.0 includes a number of additional algorithms that can be used to study sequences and study conditional behaviors (e.g., to study the frequency of or time allocated to walking while chewing gum), as well as algorithms to combine multiple results files and those to study inter- or intra-observer reliability . JWatcher is written in Java[TM] and will run on almost any microcomputer capable of providing a Java Virtual Machine[TM] and has been tested on both Windows[TM] and Macintosh[TM] systems. The legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while the newest release (Version 1.0) works well on Macintosh OS-X and Windows XP systems.
• LucidCentral.org (487)
  Home of the Lucid family of software. Lucid is a flexible and powerful knowledge management tool that helps users make an identification or diagnosis. Lucid tools are powerful and highly flexible knowledge management software applications designed to help users with identification or diagnostic tasks. Lucid software is a special type of expert system, specifically designed for identification and diagnostic purposes, which enables expert knowledge to be “cloned” and distributed to a wide audience via CD or the Internet.
• MacAnova: Statistical Analysis and Matrix Algebra (203)
  In spite of its name, MacAnova is not just for Macintosh computers and not just for doing Analysis of Variance. MacAnova is a free, open source, interactive statistical analysis program for Windows, Macintosh, and Linux written by Gary W. Oehlert and Christopher Bingham, both of the School of Statistics, University of Minnesota. MacAnova has many capabilities but its strengths are analysis of variance and related models, matrix algebra, time series analysis (time and frequency domain), and (to a lesser extent) uni- and multi-variate exploratory statistics.
• Morpho - Data Management Software (390)
  Morpho allows you to create and manage your data, and to share it with others. It was created to provide an easy-to-use, cross-platform application for accessing and manipulating metadata and data (both locally and on the network). Morpho allows ecologists to create metadata, (i.e. describe their data in a standardized format), and create a catalog of data & metadata upon which to query, edit and view data collections. Produced by the Knowledge Network for Biocomplexity Project at ecoinfromatics.org. [Linux, MacOSX 8&9, Windows]
• Papers (228)
  Best described as iTunes for PDFs, Papers provides a single application to manage and access your digital reprint collection. You can seek, download, archive, and organize your articles in "smart folders". In addition to adding files by dragging and dropping the PDFs, Endnote, RefMan, BibTex and Connotea libraries can be imported. Originally limited to being able to only search PubMed, you can now search with Google Scholar, Scopus, and Web of Science, with more search engine plugins on the way. Winner of the 2007 Apple Design Award for 'Best Mac OS X Scientific Computing Solution'
• Picses Conservation - Analytical Software (756)
  Software for community ecology, statistics, sampling and database applications.
  Community ecology:Community Analysis Package; Ecom; Species Diversity & Richness III; Community Sequence Analysis
  Statistics: Axis; Fuzzy Grouping
  Sampling analysis: Density from Distance; Hedgerow Assistant; Removal Sampling; Simply Growth; Simply Probit; Simply Tagging
  Databasing, etc.: Pisces Library Manager
  NOTE: this replaces the links to the packages "Species Diversity and Richness and Simply ...." [windoze only]
• Population Analysis Software Archive - USGS-Pawtuxent River Wildlife Research Center (483)
  A collection of specialized software tools for population analysis and sampling design. Programs are in a wide variety of formats, from FORTRAN to BASIC to web-based Java applets.
• R (459)
  A language and environment for statistical computing and graphics, R is similar to the award-winning S system. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, C, C++ and Fortran code can be linked and called at run time. [Linux Mac/OS8+/OSX PC/Win]
• SAS Institute, Inc. (417)
  product information; technical support documents; FTP site, sample programs.
• The Nestedness Calculator (376)
  The Nestedness Calculator measures the extent of the order present in nested presence-absence matrices, as well as provides a risk assessment of the extinction probability of the various species' populations isolated on islands of fragmented habitat. This Windows-based (Windows 3.x, 95, 98 or NT4) program will calculate the "temperature" (signal to noise) of nestedness order within a species presence-absence matrix (up to 4 billion cells). Included are 294 presence-absence matrices taken from the primary ecological literature. Some of the matrices are highly nested, some are not, while others are anti-nested due to factors such as "checkerboarding" and allopatric speciations. Also available is the companion paper by the author: Atmar, W. and B.D. Patterson. 1993. The measure of order and disorder in the distribution of species in fragmented habitat. Oecologia 96:373-382.
• TNT - Geospatial Analysis (427)
  TNTmips is a professional geospatial analysis system providing a complete self-contained integration of a fully featured GIS, RDBMS, and automated image processing system with CAD, TIN, surface modeling, map layout and innovative data publishing tools. All this capability is available in a single integrated system at one price with an identical interface, functionality, and geodata structure for use on Mac OS X, Windows, Sun Solaris, and popular Linux platforms. Also available is full featured freeware version, TNTlite, which is restricted in project size.
• Vensim Simulation Software (622)
  Vensim is used for developing, analyzing, and packaging high quality dynamic feedback models. Models are constructed graphically or in a text editor. Features include dynamic functions, subscripting (arrays), Monte Carlo sensitivity analysis, optimization, data handling, application interfaces, and much more. Ventana Systems also provides the Molecules software, for constructing system dynamics models from "chunks" or molecules of system dynamics structure. Vensim PLE (Personal Learning Edition) is available free for academic use. Windows and Mac OS9.

Database

• BioLink (479)
  BioLink manages taxon-based information such as nomenclature, distribution, classification, ecology, morphology, illustrations, multimedia and literature. Specimen-based information (the "Who, What, When and Where" information) includes collection sites, collectors and collection dates, museum storage locations, loans and accession and catalogue numbers. For those involved in surveys, BioLink records information on ecological characteristics, traps and bulk samples. Existing data can be easily imported into BioLink using the Import Wizard.Supported formats include tab-delimited text files, Excel spreadsheets and Access and DBF databases. [PC/Win]
• Biota: The Biodiversity Database Manager (478)
  Specimen-Based, Biological Data and Collections Management Software for Individuals, Institutions, and Projects.
• BRAHMS (379)
  BRAHMS is database software for botanical research and collection management. It provides comprehensive support with collection curation and a wide range of taxonomic and biodiversity research. With BRAHMS, you can create different types of products from simple lists, loan forms, labels, tables, checklists, graphs and maps to more complex indexes and monographic publications formatted for specific journals.[PC/Win]
• MANTIS (515)
  "Mantis" is a new biological database manager that features the ability to store taxonomic and specimen data, images and sounds,and it has built in managers of citations, specimen loans, and addresses. This database is Internet-ready and comes bundled with a set of customizeable HTML pages. [ Mac/OS9-/OSX PC/Win]
• Taxis (565)
  TAXIS is a database management system designed for biologists (professionals as well as amateurs). The main purpose of this software is to provide an interactive and user-friendly tool to facilitate processing of taxonomic information: keeping records of biological collections, studying collected specimens by recording characters, photographs, drawings, etc. TAXIS will automatically serve as an interactive identification system that make use of recorded characters, taxa and images. The structure of TAXIS database makes it possible to use it for any group of organisms. [PC/Win]

Graphics

• GMT - Generic Mapping Tools (429)
  GMT is a free, open source collection of ~60 tools that allow users to manipulate (x,y) and (x,y,z) data sets (including filtering, trend fitting, gridding, projecting, etc.) and produce Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots through contour maps to artificially illuminated surfaces and 3-D perspective views in black and white, gray tone, hachure patterns, and 24-bit color. Unix is the native platform, but will run under Windows and MacOS and OS/2. This is the software that drives the Online Map Creator (see NABSLinks - Images:Maps)
• GRACE plotting software (389)
  Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace runs on practically any version of Unix. As well, it has been successfully ported to VMS, OS/2 and Win9*/NT (some minor functionality may be missing, though).
• ImageJ (425)
  ImageJ is a general-purpose image-process software inspired by the well-known NIH Image software. It is written in Java, meaning that it can run on any platform. ImageJ can read and write various formats of an image file (e.g., TIFF, GIF, BMP); display capabilities: zooming, contrast and brightness controls; Copy/paste; provide some statistical information: measurement, histogram, etc; includes standard image processing functions: filtering, morphology, etc; extensible by adding plugins.
• iMap2 (462)
  iMap 2 is a powerful but easy-to-use program designed for mapping large amounts of latitude / longitude data. iMap works with different kinds of picture maps (BMP, TIFF, JPEG, PICT, GIF or PNG), ensuring appealing and information-rich maps. The program is supplied with a plethora of ready-to-use maps. Additional maps can be downloaded from the Internet, exported from GIS software or they can be scanned. The calibration of the maps can be done from within iMap. (Mac OSX)
• USAPhotoMaps (392)
  USAPhotoMaps downloads aerial photo and topo map data from Microsoft's free TerraServer Web site, saves it on your hard drive, and creates seamless maps from it. You can: Scroll and zoom; See the latitude/longitude; Add waypoints, routes, and text; Jump to any waypoint or latitude/longitude in the U.S.A.; Transfer waypoints, tracks, and routes to and from most GPS receivers; See your GPS location. [Windoze 98 and above]

Modeling

• NetLogo (371)
  NetLogo is a programmable modeling environment for building and exploring multi-level systems. It is one of a class of new "object-based parallel modeling languages" (OBPML). NetLogo allows you to control the behavior of thousands of objects in parallel. Each object has its own variables and state. This allows one to model the behavior of distributed and probabilistic systems, often systems that exhibit complex dynamics.
• RangeModel (452)
  A Monte Carlo simulation tool for visualizing and assessing geometric constraints on species richness.RangeModel is an animated, graphical application designed to demonstrate the mechanism behind the mid-domain effect. RangeModel is intended as a companion to: Colwell, R. K., and D. C. Lees. 2000. The mid-domain effect: geometric constraints on the geography of species richness. Trends in Ecology and Evolution 15, 70-76.You need not supply any data to run RangeModel or to learn from it. The program includes several theoretical range/midpoint distributions as built-in options. In addition, RangeModel can be used as a simple analytical tool, to produce the expected distribution of species richness, given random placement of empirical range distributions and range midpoints. You can import your own empirical or theoretical data into RangeModel from plain text files and export results for analysis in spreadsheet or statistical applications.