On-line Analytical Palaeobiology Resources

Welcome to the new on-line archive of resources for analytical palaeobiology. The pages here contain a set of links to a range of resources and data for analytical palaeobiology. The list is unapologetically biased towards sites that I know about and have found useful in the past. The programming languages and individual websites listed are likewise biased. So don't be offended if I haven't included your site or favourite programming language.

I've tried to group the sites into some sort of logical order, but this may change over time. I've tried to emphasize sites that have freeware or open source tools, but some of the sites do contain proprietary software as well.

I'm interested in how great a demand there is for such information among people passing through the Pal Ass website, so if you make use of any of the resources on this page, please let me know via meetings@palass.org. Levels of interest will help me gauge how much effort should go into this page.

I've tried to cover large sites which already have additional archives of other sites that I hope will be useful.

If you have a link or site that you think should include in these pages, please contact me. I'd also be interested in whether or not users would like a list of useful books and journal articles added to the site.

The Mother Lodes
These sites have large amounts of useful information and programs.

SUNY morphometrics site
Your one-stop site for morphometrics resources on the web. The SUNY site has large lists of programs and data sets, a glossary of morphometric terms, and lots of other information. Link

International Biogeography Society (IBS)
The IBS website has very comprehensive lists of resources for biogeographers. Given the wide scope of biogeography you can find tools for ordination methods, cladistics, ecological data handling and a range of related topics. Link

General Geological software lists
This site deals with Macintosh software for general geological uses Link

Paleonet
Paleonet has some links to software resources. Link

Biological Collection Management Software
A site that gathers together many collection management tools Link

Paleobiology Source Code Archive
This is an archive of software code and programs. Link

Ordination Methods for Ecologists
This site is run by Michael Palmer, an ecologist at Oklahoma State University. The site has a lot of discussion about the behaviour of different ordination techniques, and advice about which techniques to use for different questions. Link

Programming Languages

Python
Python is an interpreted language that is fairly easy to learn. There are many tutorials available and a good range of books. Link

Scientific Python (site dedicated to all scientific uses of Python)
This site details the use of Python across the sciences Link

Perl
Perl is a language used for scripting (automation of computer tasks) and for some web design tasks. Perl has strong similarities to Python Link

R-project (a freeware version of S-plus)
R is a significant resource for anyone who wants powerful statistics tools without paying hundreds of pounds/dollars. R is command-line driven, but the investment in time is worth it. R has a very large user community and there are many add-on modules that cope with specific analytical tasks Link

Package for Analysis of Space-Time Ecological Series (runs under R)
One example of a package written in R for tackling specific analyses. Link

On-line databasing tools

MySQL MySQL is a powerful relational databasing tool. Link

PHP PHP is usually used for handling input and output to webpages in conjunction with MySQL. Link

Sites of individual researchers with resources

Øyvind Hammer (Co-author of PAST)
Øyvind Hammer and D. A. T. Harper jointly developed PAST, but Øyvind has done a lot of work in computational palaeontology. His personal site has a lot of information about his other projects Link

Phillipe Legrende (Author of Numerical Ecology)
Legrende is an ecologist who has published a number of computer programs and books dealing with a range of analytical techniques. Link

Shanan E. Peters
Shanan's site has some on-line calculation tools. Link

Sepkoski's Genus data base (maintained by Shanan Peters)
This site is a direct port of the Sepkoski (2002) genus-level database. The site can do some analyses for you as well. Link

Page Lab
A variety of software packages written by Roddy Page and co-workers to address a range of questions. Much of the software is useful for molecular phylogenetics and biogeography Link

Chris Scotese's Paleomap site
Chris has made a large number of palaeogeographic resources available through his website. Chris also has various tools that interact with ArcView GIS. Link

e-Science projects

GEON project
GEON is a collection of 'federated' databases which means that there is some interoperability among the databases, despite the fact that each data base is maintained by separate groups. Link

UK National Institute for Environmental e-Science (NIEeS)
NIEeS is the arm of UK e-Science that deals with environmental science in the broadest sense. NIEeS is a useful place to go and learn about web-based applications and tools to help with analysis and distribution of data. A number of seminars and workshops are run throughout the year. Link

UK National e-Science Centre
e-Science is an emerging field that is mainly concerned with linking computers together for large computations, and as a means for linking researchers together through cyberinfrastructure to reduce the need for physical travel. Link

Other tools useful for morphometrics

Image J (successor to NIH Image)
ImageJ is a tool for image analysis. It can be used for a lot of morphometric data gathering, but is not as easy to use as some propreitary systems. You can combine ImageJ with PAST to do geometric morphometrics for very limited cost. Link

Shell Axis
A program for studying shell coiling. Link

On-line biodiversity projects

Global Biodiversity Information Forum (GBIF)
A major clearing house for biodiversity information and data. Link

National Biodiversity Network (NBN)
NBN is the UK portal to GBIF. Much of the ecological information is linked to Ordnance Survey grid information, and has great potential as a test data set for spatial analyses. Link

Panama Paleontology Project (PPP)
The PPP is a long-term project studying the rise of the Panama Isthmus. The PPP represents one approach to on-line palaeontological databasing that involves records being tied to specimens, rather than the literature-based approach of the Paleobiology Database Project. Link

Paleobiology Database Project (PBDB)
The PBDB is an attempt to assemble a literature-based record of palaeontological data on taxon occurrences and abundances . The public are free to download data and use many of the tools available to the researchers. Link

The Fossil Record website
Another website that has a large taxonomic dataset, originally developed as a companion to "The Fossil Record 2". The website and Fossil Record project are currently being updated, so check back regularly for changes. Link

Paleomath 101 homepage Link

Newsletter 56: Regression 2
Discussions of the capabilities and limitations of Excel

• HELSEL, D.R. 2002. Is Microsoft Excel an adequate statistics package? Link
• GOLDWATER, E. 1999. Using Excel for statistical data analysis. Link
• POTTEL, H. 2002. Statistical flaws in Excel Link

Newsletter 61: Minding Your Rs and Qs Principal Co-ordinates (PCO) packages recommended by N. MacLeod

• NTSYS Link
• Syn-Tax Link

Web resources for Peter Forey's Cladistics 101 Cladistics for Palaeontologists Link

PAUP Link

PAST Link

• Google Earth Link
• ArcGIS Explorer. This is ESRI's 'virtual globe' offering. The main ESRI site contains information about other products Link
• NASA World Wind Link
• Open Layers (an open-source Javascript library) Link
• Reading e-Science Centre. The projects here are focused on environmental sciences, but some tools could have applications in palaeontology. Link
• Link to NIEeS workshop 'Google Earth and other geobrowsing tools in the environmental sciences workshop 2-3rd April 2007'. Many of the presentations given at the meeting have been posted on this page. Link
• DIVA-GIS. A powerful free GIS program. Link