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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.

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. (2014): CREST (Climate REconstruction SofTware): A probability density function (PDF)-based quantitative climate reconstruction method. In PDF. Clim. Past, 10: 2081-2098. See also here.

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.

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).

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.

! Eric C. Grimm, Illinois State Museum, Research and Collections Center, Springfield, IL: Tilia Graph. See also:
Tilia & Tilia Graph - Frequently Asked Questions.
Data-handling Methods for Quaternary microfossils. (by K.D. Bennett).

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

! 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.

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.

S. Lautenschlager, Software Sustainability Institute: A Digital (R)evolution in Palaeontology.

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.

R. Petschick, Geologisch-Paläontologisches Institut, J.W. Goethe University, Frankfurt am Main, Germany: Assorted Macintosh software and some more links relevant for geoscientists.

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.

! C. Price et al., School of Plant Biology, University of Western Australia, Perth: LEAF GUI (Leaf Extraction and Analysis Framework Graphical User Interface). This software is designed chiefly for plant biologists and ecologists who wish to analyze the macroscopic structure of veins in leaves. Can be used for all images (TIF, GIF, JPG, BMP, PNG) with high resolution and good contrast between veins and the background (with visible minor veins). LEAF GUI is free for academic use (registration needed). See also:
Charles A. Price et al. (2011): Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles. Plant Physiol., 155: 236-245.

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

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)

TreeView. Tree drawing software for Apple Macintosh and Windows.

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. In PDF, Geologos, 15: 181-188.

Carl Zeiss Microscopy: Microscope Software AxioVision LE (AxioVision LE for Windows, available as 32-bit and 64-bit version). Freeware imaging software for image analysis and digital microscopy.









Home / Software / Software for Botany and Biology


Categories
Downloadable Ternary Plot Programs (shareware)@
Ternary Plotting Programs for Sale@
! Geostatistics@


Software for Botany and Biology


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

Chris Creevey & James O. McInerney, Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth: Clann. Construction of Supertrees and exploration of phylogenomic information from partially overlapping datasets. This software program is free and it implements the greatest number of phylogenetic supertree methods.

Joe Felsenstein, Department of Genetics, University of Washington, Seattle, Washington: Phylogeny Programs. List of packages arranged by methods available, cross-referenced by method and by computer systems. The programs listed here include both free and non-free ones.

! FSF/UNESCO Free Software Directory (a project of the Free Software Foundation, Inc.(FSF), Boston, MA, and United Nations Education, Scientific and Cultural Organization, UNESCO). Useful free software that runs under free operating systems - particularly the GNU operating system and its GNU/Linux variants. There are 4,386 packages indexed. Go to: Biology

! Eric C. Grimm, Illinois State Museum, Research and Collections Center, Springfield, IL: Tilia Graph (TGView Version 2.0.2). It is a full-featured program with complete text - editing capabilities, sediment-column drafting capabilities with Trolls-Smith and bit-map patterns, many different options for zones, dates, grouping of pollen curves, etc. See also:
Tilia & Tilia Graph - Frequently Asked Questions.
Data-handling Methods for Quaternary microfossils. (by K.D. Bennett).

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

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.

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.

SPSS Inc.: Today, more than 250,000 organizations use SPSS, a software for desktop analysis, to create and distribute information for better decision making. Fully functional demos of SIGMAPLOT and DELTAGRAPH.

Stefan Steinhaus, University of Frankfurt: The Scientific Web. Scientific Web presents an index of scientific programs in chemistry, mathematics, statistics, optimization, data acquisitions and others including detailed product information, addresses of producers and distributors, product announcements, links to other Internet addresses, usergroups, etc.

TAXONOMIC TOOLS BY COMPUTER 2 (TTBC2)










Home / Software / Software for Geology and Geo-Software Indexes


Categories
Categories
Software for Palaeontology
Software for Botany and Biology
Software of all Topics
Freeware
Tutorials, Tips and Tricks to selected Writing and Drawing Computer Programs@
Grafic Software@
! Geostatistics@


Software for Geology and Geo-Software Indexes


Mineralogy Club of Antwerp, Belgium: Mineralogy Software. Annotated index to some mineralogy, gemmology and crystallography software and database.

ATHENA, University of Geneva: Shareware related to science. Briefly annotated list.

Department of Petroleum and Geosystems Engineering, University of Texas, Austin: Geoscience and Engineering Software. A collection of software related to various Geoscience and Engineering fields. Access to Computer Oriented Geological Society, Cornell University, Geology Department, GSLIB, Int. Association of Math. Geologists, U.S. Department of Energy codes, U.S. Geological Survey codes.

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.

S. Baum, Dept. of Oceanography, Texas A&M University: Software for Graphics and Data Analysis.

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.

Bob´s Rock Shop: Software for Rockhounds. Web page provides a mineral database and identification software and compression software.

Arthur B. Busbey, Department of Geology, Texas Christian University, Fort Worth, Texas: Macintosh Geological Software. Index in alphabetical order of the product name.

John C. Butler, Department of Geosciences, University of Houston: Another Node On the interNet, (ANON). Geoscience Software Resources on the Web.

Comsol: FEMLAB (in German). CD "Model Library" free of charge. Including a chemical engineering module, an electromagnetics module, and a structural mechanics module.

E.R. Crain, Rocky Mountain House, Alberta, Canada: CRAIN'S PETROPHYSICAL HANDBOOK. An Online eText Reference Manual on integrated petrophysics and well log analysis with META/LOG shareware software. Free access, registration procedure required.

dmoz open directory project: Science: Software.

earthnet online. Service provided by the European Space Agency - ESRIN, Frascati, Italy. After registration procedure various accesses, e.g. to the SOFTWARE GALLERY to download software for reading satellite products or to check satellite routing, or to images.

! Earth Science Australia, Mineral Resources (copyright by American Geological Institute): Freeware Downloads. Most programs are self-extracting .exe files, but some programs offer extra features in shareware versions.

EJGE Magazine, World Wide Web of Geotechnical Engineers: Geotechnical Software Resources on the Net.

Entrance Software, Houston, TX: BSLS Online 1.0. Biostratigraphic Lithostratigraphic Column Generator. BSLS Online facilitates the construction of biostratigraphic and lithostratigraphic column charts. Free of charge!

! FSF/UNESCO Free Software Directory (a project of the Free Software Foundation, Inc.(FSF), Boston, MA, and United Nations Education, Scientific and Cultural Organization, UNESCO). Useful free software that runs under free operating systems — particularly the GNU operating system and its GNU/Linux variants. There are 4,386 packages indexed. Go to:
Geology.

Anthony Gary and Robert Ehrlich, Center for Industrial Imaging, Energy and Geoscience Institute, University of Utah: Technical Alliance for Computational Stratigraphy (TACS). TACS is developing a biostratigraphic workstation capability by building on existing applications and technologies, and through new technology development.

The Geotechnical and Geoenvironmental Software Directory. A directory of geotechnical software, engineering geology software, hydrogeology software, geoenvironmental software, data analysis software and data visualisation software. Excellent!

GeoWeb Services Inc., Houston: GeoWeb Service Interactive. The goal of the site is to provide the best possible internet resource for serving the needs of all companies and professionals. See: Search Software, or Java Resources.

gINT Software, for Geotechnical and Geoenvironmental Professionals. gINT is one of the leading brand of integrated geotechnical and geoenvironmental software, with over 5,500 licensees in 45 countries and a 18-year track record of success.

Institute for Geosciences, Johannes Gutenberg University, Mainz: Geoscience related Software.

Daniel Marshall, Department of Earth Sciences, Simon Fraser University, Vancouver, Canada: Some Programs/Utilities, These are programs written by Daniel Marshall for general use, please feel free to copy them and/or give them to colleagues and friends.

Institut Méditerranéen d´Ecologie et de Paléoécologie, Marseille. PSIMPOLL and GPALWIN free to download! This programs runs only on Windows 95/98 or NT4.

The Microbeam Analysis Society: Microscopy & Micoanalysis Software Library.

MinServ (Geoscience Software), Wantirna, Australia.

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

Oil Survey: Geo-software, engineering resources.

Yvan Pannatier, University of Lausanne (Switzerland): Geostatistical Software for the PC. This site presents Microsoft Windows and DOS software which have been found useful for teaching spatial data analysis and geostatistic.

Price Watch: Street Price Search Engine. PriceWatch provides street prices for computers, CPUs, memory, storage, multimedia, input devices, output devices, accessories, connectibity products, software and various electronic products. As a kind of "robotic" service, it scans merchant prices and posts prices.

RockWare. Geology software for civil engineering, education, environmental applications, hydrology, mining, petroleum, and structural geology. Free downloads and utilities!

Schlumberger Limited (an oilfield services provider): Free Software Utilities. Tools for viewing and customizing your data.

The Soft Earth: Part 2 - Software and Software Sites. One of the most comprehensive indexes of annotated Geoscience Software. The Soft Earth is mirrored weekly at Mikael Niklasson´s page in Sweden.

Tim Spink, The Geotechnical and Geoenvironmental Software Directory: Useful World Wide Web links. This page contains links to WWW software sites, directories of software and/or links to other sites. u!

SPSS Inc.: Today, more than 250,000 organizations use SPSS, a software for desktop analysis, to create and distribute information for better decision making. Fully functional demos of SIGMAPLOT and DELTAGRAPH are available.

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.

TexaSoft: Winks. Winks makes statistical data analysis understandable and easy to perform. Available for Windows 3.1, 95, 98 and NT.

Dave Waters, Department of Earth Sciences, University of Oxford: Geological Software. An annotated bookmark list.

Pierre A. Zippi, Garland, Texas: PAZ Software. Geology, biostratigraphy, earth science software, scientific software for Macintosh computers (with costs).










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This index is compiled and maintained by Klaus-Peter Kelber, Würzburg,
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Last updated October 08, 2016















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