Home / Palaeobotanical Tools / Software for Palaeontology

AASP - The Palynological Society, Paleopalynology and Stratigraphic Palynology. Scroll down to: Databases and data sets, Ravn, R.L. 1998. TAXON: a DOS hypertext database of 30,000 species of palynomorphs with references and annotations. [revised 1999]. AASP Data Committee, PALYDISK 17. 6 Megabytes!

AWI, Foundation Alfred Wegener Institute for Polar and Marine Research and MARUM, Center for Marine Environmental Sciences, Bremen: PANGAEA. The information system PANGAEA is a public data library on the Internet aimed at archiving, publishing and distributing geocoded data with special emphasis on environmental, marine and geological research. AWI and MARUM have commited to operate PANGAEA on a long-term basis. Go to: Software. The Software on this page is provided by the PANGAEA-Network for the visualization, exploration and interpretation of scientific data. The tools are freeware.

Keith Bennett, Queen's University, Belfast, Northern Ireland, UK. Psimpoll and Pscomb programs for plotting and analysis. This page provides access to programs relevant for acquiring, plotting, and analysing palaeoecological data, including (but not only) pollen data.

W. Berendsohn, Biodiversity Information Standards (TDWG): TDWG Subgroup on Biological Collection Data, Software for Biological Collection Management. This page lists software which is used in collection management.

! Museum of Paleontology, University of California, Berkeley, CA: Databases and Software Lists. See also: Phylogenetics Software Resources.

! BioDeepTime:
This project seeks to address one of the central challenges in biodiversity science by compiling and harmonizing ecological time series from modern and fossil sources to investigate how biological dynamics and drivers vary across timescales ranging from months to millions of years. Note likewise here.
Please take notice:
! J. Smith et al. (2023): BioDeepTime: A database of biodiversity time series for modern and fossil assemblages. Open access, Global Ecol Biogeogr.
Note table 1: Approximate temporal grain (the amount of time represented in a sample) for time series, number of time series and number of samples from source databases included in BioDeepTime.
"... The BioDeepTime database enables integrated biodiversity analyses across a far greater range of temporal scales than has previously been possible. It can be used to provide critical insights into how natural systems will respond to ongoing and future environmental changes as well as new opportunities for theoretical insights into the temporal scaling of biodiversity dynamics ..."

V. Blagoderov et al. (2012): No specimen left behind: industrial scale digitization of natural history collections. In PDF, Zookeys, 209: 133-146.

E. Callaway (2015): Computers read the fossil record. Palaeontologists hope that software can construct fossil databases directly from research papers. In PDF, Nature Toolbox. See also here.

M. Chevalier et al. (2022): crestr: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Free access, Climate of the Past, 18: 821–844.

M. Chevalier et al. (2014): CREST (Climate REconstruction SofTware): A probability density function (PDF)-based quantitative climate reconstruction method. Free acces. Clim. Past, 10: 2081-2098.

! Chip (in German):
Vollversion: Photoshop CS2. Photoshop CS2 free of charge!

Cladistics.com: Software for Systematics. Downloadable software, e.g. WinClada, NONA, TNT, Trees.

! CLAMP Online (Climate Leaf Analysis Multivarite Program). This site is the result of an ongoing collaboration between the Institute of Botany, Chinese Academy of Sciences, Beijing, and the Open University UK.
How you can use foliar physiognomy (leaf architecture) to determine ancient climates from fossil leaves or explore the relationship that exists between leaf form and climate. CLAMP is a multivariate statistical technique that decodes the climatic signal inherent in the physiognomy of leaves of woody dicotyledonous plants. See especially:
! Teaching Materials.
Older CLAMP websites are available through the Internet Archive´s Wayback Machine:
Robert A. Spicer, The Warm Earth Environmental Systems Research Group: Plant Fossils as Climatic Indicators. Go to: Climate Leaf Analysis Multivariate Programe (CLAMP). An introduction to the use of leaf architecture for determining past climatic conditions.

CollectiveAccess. This is a highly configurable cataloguing tool and web-based application for museums, archives and digital collections. Available free of charge!

Mitch Covington, Tallahassee, Florida: BugWare, Inc. BugWare maintains an extensive library of paleontological software to collect, store, graph, convert, etc. paleontological data, designed for Windows 95/98/NT. This software e.g. displays photos of nannofossils and descripions together and allows the comparison of two different fossils simultaneously. The fossils can be arranged in a tree fashion by family or group, genus and species. The software part (BugCam) can be adapted for other fossils.

! J.A. Cunningham et al. (2014): A virtual world of paleontology. Trends in Ecology & Evolution, 29: 347-357.

Dave Dobson, Guilford College, Greensboro, NC: SimpleClade. This is is a software program that allows simple cladistic analysis with a graphical user interface.

! Joe Felsenstein, Department of Genome Sciences and Department of Biology, University of Washington, Seattle: PHYLIP. 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. Go to: Phylogeny programs available elsewhere. Links to 383 phylogeny packages (free and non-free ones) and 52 free servers.

J.T. Flannery-Sutherland et al. (2022): fossilbrush: An R package for automated detection and resolution of anomalies in palaeontological occurrence data. Open access, Methods in Ecology and Evolution, 13: 2404-2418.
Go to: cran.r-project.org: fossilbrush: Automated Cleaning of Fossil Occurrence Data. See also here.
! Access to the Paleobiology Database.

! S.G.A. Flantua et al. (2023): A guide to the processing and standardization of global palaeoecological data for large-scale syntheses using fossil pollen. Open access, Global Ecol. Biogeogr., 32: 1377-1394.
Note figure 1: Essential data processing components needed to create a standardized, harmonized, palaeoecological dataset compilation before macro-scale data analysis.
Figure 3: Summary figure of FOSSILPOL workflow providing an overview of the inputs, main workflow steps and outputs.
"... With our FOSSILPOL workflow and R-package, we provide a protocol for optimal handling of large compilations of fossil pollen datasets and workflow reproducibility ..."

Pablo Goloboff, Steve Farris and Kevin Nixon: TNT. TNT stands for Tree Analysis Using New Technology a program that can analyse large data sets (i.e. 300-500 taxa) in reasonable times (minutes to find a shortest tree, hours to produce a reliable consensus).

Good Calculators (by John Sanders and Andrew Stacy). Free calculators. See especially:
! Mathematics Statistics and Analysis Calculators.

Felix M. Gradstein, Museum for Geology and Paleontology, University of Oslo, Norway, and Frits P. Agterberg, Department of Geology, Ottawa University, Canada: RASC & CASC. Tools for biostratigraphic zonation and correlation. RASC is an acronym for ranking and scaling of biostratigraphic events; CASC stands for correlation and standard error calculation.

! Henri D. Grissino-Mayer, University of Tennessee, Knoxville, Tennessee: Software to Analyze Tree Rings. An annotated link list.

S. Guo et al. (2023): A new method for examining the co-occurrence network of fossil assemblages. Free access, Communications Biology, 6.
Go to: TaphonomeAnalyst.

! Øyvind Hammer, Paleontological Museum, University of Oslo: PAST. PAST is a free, easy-to-use data analysis package aimed at paleontology. Inspired by PALSTAT, it includes common statistical, plotting and modelling functions, e.g. a spreadsheet-type data entry form, graph, scatter, histogram, ternary and survivorship plots, etc.
See also here.

T.A. Hegna and R.E. Johnson (2016): Preparation of Fossil and Osteological 3D-Printable Models from Freely Available CT-Scan Movies. In PDF, Journal of Paleontological Techniques, 16: 1-10.

K. Holt et al. (2011): Progress towards an automated trainable pollen location and classifier system for use in the palynology laboratory. In PDF, Review of Palaeobotany and Palynology, 167: 175-183.
See also here.

E.M. Knutsen and D.A. Konovalov (2024): Accelerating segmentation of fossil CT scans through Deep Learning. In PDF, Scientific Reports, 14.
See likewise here.

Hannes Löser, Hermosillo, Sonora, México: PaleoTax. PaleoTax is a database management system to record taxonomic, geographic and stratigraphic data in biology and palaeontology and dedicated to taxonomists.

Hannes Löser (Dresden; Hermosillo), Jürgen Kullmann (Tübingen) and Olga Dietl (Stuttgart): Datenbanken in der Paläontologie (in German). This expired link is available through the Internet Archive´s Wayback Machine.
See also here (Google books) and there.

A. Lugowski (Computer Science Dept., Univ. Calif. Santa Barbara) and J. Ogg (Dept. Earth and Atmos. Sci., Purdue University): TimeScale Creator This is a free JAVA package to explore and create charts of any portion of the geologic time scale from an extensive suite of global and regional events in Earth History.

Wayne P. Maddison and David R. Maddison: Mesquite. A modular system for evolutionary analysis. Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

! Norman MacLeod, Natural History Museum, London: PalaeoMath. Aspects of quantitative analysis in paleontological contexts. Each essay (from the Palaeontological Association Newsletter since 2004) is written for the novice data analyst, especially those who always wanted to gain knowledge of this subject, but never had the opportunity to do so and haven´t managed to make much progress through self-education. Including some MS Excel spreadsheets providing examples and data.

NOAA Paleoclimatology Program, National Geophysical Data Center, National Oceanic and Atmospheric Administration (NOAA), Boulder, Colorado: Free Software. A link list.

NOAA Paleoclimatology: Free Software. A link list.

The Open Source Paleontologist (Blog): Statistics Software. An annotated link directory.

! The Palaeontological Association: Online analytical resources for palaeobiology. A annotated link list.

! Paleotax Verlag Dresden, Germany: PaleoTax. PaleoTax is a universal database program and excellent tool for taxonomists in biology and paleontology. Free of charge.

Rod Page, Division of Ecology and Evolutionary Biology, Faculty of Biomedical and Life Sciences, University of Glasgow: COMPONENT 2.0. Now free of charge! This is a computer program for analysing evolutionary trees.

! K.M. Pryer et al. (2020): Using computer vision on herbarium specimen images to discriminate among closely related horsetails (Equisetum). Open access, Applications in plant sciences, 8.

I. Rahman, WordPress: Virtual Palaeontology: What´s It All About?
Virtual Palaeontology.

F. James Rohlf, Department of Ecology and Evolution, State University of New York, Stony Brook, NY: Morphometrics at Stony Brook. Server contains news and files related to the field of geometric morphometrics. See also: http://life.bio.sunysb.edu/ee/rohlf/software.html

A.J. Rowe and E.J. Rayfield (2022): The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis. Open access, PeerJ, 10, e13760. doi:10.7717/PEERJ.13760/SUPP-1.

! J. Schindelin et al. (2012): Fiji - an Open Source platform for biological image analysis. Open access, Nat Methods, 9: 10.1038/nmeth.2019.

C.A. Schneider et al. (2012): NIH Image to ImageJ: 25 years of image analysis. In PDF, Nature methods.

P. Schols et al. (2010): CARNOY: A new digital measurement tool for palynology. In PDF, Grana, 41: 124-126.

! Robert A. Spicer, The Warm Earth Environmental Systems Research Group: Plant Fossils as Climatic Indicators. Go to: Climate Leaf Analysis Multivariate Programe (CLAMP). An introduction to the use of leaf architecture for determining past climatic conditions.

Evgeny Stambulchik, WIS Plasma Laboratory: Grace. 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.

! M.D. Sutton et al. (2012): SPIERS and VAXML; A software toolkit for tomographic visualisation and a format for virtual specimen interchange. In PDF, Palaeontologia Electronica, 15.

David L. Swofford, Florida State University: PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta. A software package for inference of evolutionary trees, for use in Macintosh, UNIX/VMS, or Windows/DOS-based formats. Provided by the Internet Archive´s Wayback Machine.
Go to: AWTY. A system for graphical exploration of Markov chain Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. See also:
Beta Documentation (in PDF).

TAXONOMIC TOOLS BY COMPUTER 2 (TTBC2).
Website outdated. The link is to a version archived by the Internet Archive´s Wayback Machine.

S. Varela et al. (2015): paleobioDB: an R package for downloading, visualizing and processing data from the Paleobiology Database. In PDF, Ecography, 38: 419-425.

Steve Wagner, Denver Museum of Nature & Science (DMNS): PaleoCollaborator A web software tool (a volunteer effort) for fossil identification/display available for free!

Adam Walanus and Dorota Nalepka: POLPAL 2004. An application for plotting pollen diagrams, counting pollen grains, and performing numerical analysis. See also here and there.

Campbell O. Webb and Michael Donoghue, Department of Ecology and Evolutionary Biology Yale University: Phylomatic. A database for applied phylogenetics. The online software takes your list of taxa, and first tries to match them by genus name to the megatree.

! Whirl-i-Gig (a software development firm working in the varied worlds of museums, biological research and conservation, natural history, material culture, and art history):
CollectiveAccess (formerly known as OpenCollection). This is a full-featured collections management and online access application for museums, archives and digital collections. CollectiveAccess is freely available open-source software.

Wired, Boone, IA: A Computer With a Great Eye Is About to Transform Botany (March 17, 2016).
See also here (Geological Society of America Abstracts) and there P. Wilf et al., Computer vision cracks the leaf code (PNAS).

P. Wolniewicz (2009): Easily-accessible digital palaeontological databases - a new perspective for the storage of palaeontological information. Free access, Geologos, 15: 181-188.
"... In order to develop an easily accessible digital palaeontological database, three steps should be followed: (1) digitization of the studied specimens, (2) acquisition of morphometric data, and (3) contribution of the data to open and searchable geoinformatic (palaeontological) databases ..."

This index is compiled and maintained by Klaus-Peter Kelber, Würzburg,
e-mail kp-kelber@t-online.de
Last updated June 08, 2025