81. Buffalo Ontology Site About two dozen links collected by the Ontology Project at the philosophy department of State University of New York at Buffalo. http://ontology.buffalo.edu/biomedical.htm

Biomedical Ontology International Conference on Biomedical Ontology The OBO Foundr y ... Medical Ontology Research For additional information, contact: Barry Smith

82. Glossary Of Phylogenetic Systematics An annotated, extensive hypertext glossary of the terminology of Phylogenetic Systematics, with a discussion and criticism of mainstream Computer Cladistics. http://www.bernstein.naturkundemuseum-bw.de/odonata/glossary.htm

Glossary of Phylogenetic Systematics with a critic of mainstream cladism , SMNS, Stuttgart, 2005 Home SGSPO Phylogeny Checklist ... MUSEUM sensu HENNIG (1959, 1982, 1984), SCHLEE (1971, 1978, 1981), AX (1984, 1988), WILLMANN (1985, 1989) and SUDHAUS & REHFELD (1992), rather than to computer-cladistics and Pattern-Cladism that seem to be more «en vogue» today. I absolutely agree with the recent critic of this mainstream cladism by WÄGELE (1994, 1996a,b) and BORICKI (1996). The presented definitions have passed several years of "evolution", but of course I would be very grateful for further suggestions, amendations and corrections by the readers. agamo-species A term for groups of primarily or secondarily uniparental (= agamic, apomiktic, asexual) organisms, that are morphologically so similar that they have been classified as a single species. These agamo-species represent entities that are fundamentally different from the biospecies of biparental organisms, since the relationships between the members of an agamo-species are exclusively hierarchical, contrary to the generally reticulate relationships within biospecies. Consequently, there is no difference between

83. Learn Plants Now! Strategies and tips for learning how to identify plants in the field. Introduction to botanical terms, checklist for plant identification, recommended resources. http://www.learnplantsnow.com/

Learn Plants Now! Strategies and Tips for Learning About Plants Home About Home Start Learning Plants ... Why Study Plants? A Personal View Whenever you return to this site, you can pick up where you left off by clicking on any of the links in this article, or you can go to the Plant Articles section in the right hand column. If you then want to see more examples of plant identification discoveries, take a look at my blog where I periodically share with you the process of learning the name of a new plant. Since I live in Panama and the ecosystem I live within is a savanna, the name of the blog is A Neotropical Savanna You are very welcome to write with questions. For contact details, see the About page. May you enjoy your journey in the plant world! Posting your comment. Language/Idioma My Blog A Neotropical Savanna Downloads Plant Profile Sheet PDF File (will be downloaded to your computer) Plant Articles Start Learning Plants 19 Basic Botanical Terms Start Learning Plant Families Books for Learning Plants ... Why Study Plants? A Personal View Search for: Subscribe in a reader Subscribe to Learn Plants Now! by Email

84. Project Linnaeus Ambitious project to classify all forms of life that exist on the planet Earth and catalog the information about them for conservation and research purposes and the pursuit of knowledge. http://projectlinnaeus.com

85. What Is Cladistics? The methods and terminology of phylogenetic systematics explained by the magazine Fossil News. http://www.fossilnews.com/1996/cladistics.html

You pick up an article in the Journal of Vertebrate Paleontology Cladistics is a method of analyzing the evolutionary relationships between groups to construct their family tree. It has been around for almost fifty years, but has really become popular in the past two decades. The principle behind it is that organisms should be classified according to their evolutionary relationships, and that the way to discover these relationships is to analyze what are called primitive and derived characters. Derived (advanced) characters are called apomorphic in the lingo of cladistics. If they belong only to the group in question, they are called autapomorphic; obligate bipedalism (two-footed walking) is an autapomorphy of hominids (people), a characteristic which we do not share with the great apes. If the derived character serves to unite two groups, it is called synapomorphic; loss of a tail is a synapomorphy of the group containing great apes and man. No animal within the group has a tail, yet our next-nearest relatives, the monkeys, do. It is important to note that the designation of primitive and derived characters has meaning only when related to the group under study. A character which is derived relative to one group may be primitive for a less inclusive group. The occurrence of fur is a derived character if one is studying all tetrapods (four-footed vertebrates), and serves to distinguish mammals from their ancestors, the reptiles. However, it is a primitive character for the group consisting only of all mammals, and is not useful for determining relationships within the Mammalia.

86. Introduction To Cladistics Cladistics is a particular method of hypothesizing relationships among organisms based on the idea that members of a group share a common evolutionary history. http://www.ucmp.berkeley.edu/clad/clad1.html

Introduction to Cladistics Methodology of Cladistics ... for Cladistics An Introduction to Cladistics This module provides a brief introduction to the philosophy, methodology, and implications of cladistic analysis. Many of the terms that you will see along the way are high-lighted, e.g., evolution , which means that they are included in the UCMP Glossary of Phylogenetic Terms . Each of these terms can be clicked on for a brief definition. After you've read through the pages on the implications and methodologies, you will be armed in the ways of cladistics. Therefore, if you dare, you can take a journey into the real world of cladistics. Should you choose to venture on this journey, pray you are well-armed with good luck and wits! Synapomorphies are the basis for cladistics Cladistics is a particular method of hypothesizing relationships among organisms. Like other methods, it has its own set of assumptions, procedures, and limitations. Cladistics is now accepted as the best method available for phylogenetic analysis, for it provides an explicit and testable hypothesis of organismal relationships. The basic idea behind cladistics is that members of a group share a common evolutionary history, and are "closely related," more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors. These

87. Fossil Halls | American Museum Of Natural History Short introduction from the American Museum of Natural History. http://www.amnh.org/exhibitions/Fossil_Halls/cladistics.html

On Exhibit Plan Your Visit Calendar Science ... If you feel this page is not displaying correctly, you may need to upgrade your browser. Plesiosaurs; painting by Charles Knight AMNH News Podcast: Global Kitchen Mixes Polar Cocktails Dracula Orchids: Celebrating Hauntingly Photogenic Natural History Goblin Spiders: Celebrating Hauntingly Photogenic Natural History About ... Traveling Exhibitions American Museum of Natural History Central Park West at 79th Street, New York, NY, 10024-5192

88. The Compleat Cladist A Primer Of Phylogenetic Procedures A book about the basics of cladistics. http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf

89. Phylodendron Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform. http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/

90. TREE-PUZZLE Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. http://www.tree-puzzle.de/

TREE-PUZZLE News Description Download ... Imprint TREE-PUZZLE: Maximum likelihood analysis for nucleotide, amino acid, and two-state data Heiko A. Schmidt Korbinian Strimmer , and Arndt von Haeseler News A book chapter about ML-based testing of tree topologies using TREE-PUZZLE and Consel has been published (April 2009): H.A. Schmidt (2009) Testing Tree Topologies. In P. Lemey, M. Salemi, A.M. Vandamme (eds.) The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing. , 2nd Edition, 381-404, Cambridge University Press, Cambridge. (ISBN: paperback: , hardcover: , datasets at www.thephylogenetichandbook.org A book chapter about ML-based tree reconstruction using TREE-PUZZLE, IQPNNI and other methods has been published (April 2009): H.A. Schmidt and A. von Haeseler (2009) Phylogenetic Inference Using Maximum Likelihood Methods. In P. Lemey, M. Salemi, A.M. Vandamme (eds.) The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing. , 2nd Edition, 181-209, Cambridge University Press, Cambridge. (ISBN: paperback:

91. NONA - A Quick Guide To The Commands A brief overview of using NONA for phylogenetic analysis. http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html

NONA A Quick Guide to the Commands The following is intended to provide a quick overview of the most commonly used commands for the phylogenetic analysis program Nona. A more complete guide is available in the document Piwe.doc that is distributed with the program and with Piwe. In the columns below, you will find the command, the abbreviation for the command, frequently used arguments (if any exist) that can be added to the command to make it more specific, and the purpose of the command and its arguments. For users that are more familiar with other programs, the equivalent command in Hennig86 or PAUP* are given. Command Abrv. Arguments Purpose PAUP * help he xxx On-line list of the commands - lists all commands -list of commands by topic -describes command "xxx" assist z Exit the program y Searching for Trees Command Abrv. Arguments Purpose PAUP* whennig wh N Creates a wagner tree. It is fast but remember - a more parsimonious tree may be found later by branch swapping N stands for the number of trees to be generated. If this is specified, the order for the taxa is randomized N times

92. Phylogenetic Analysis By Maximum Likelihood (PAML) Phylogenetic analyses of DNA or protein sequences using maximum likelihood. http://abacus.gene.ucl.ac.uk/software/paml.html

Phylogenetic Analysis by Maximum Likelihood (PAML) Ziheng Yang Table of contents Introduction How fast is my new computer? Get the benchmark and save it as speed2.tar.gz Bug alert Downloading and setting up PAML Some notes about running programs in PAML To ask questions, go to The PAML discussion site . Old posts are at Genetics Software Forum PAML Manual (pamlDOC.pdf) PAML FAQs (pamlFAQs.pdf) Old versions of paml ... Questions and Bug Reports Introduction PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc. This document is about downloading and compiling PAML and getting started. See the manual ( pamlDOC.pdf

93. Mesquite Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms. http://mesquiteproject.org/mesquite/mesquite.html

If you're looking for Mesquite Software, Inc. or its CSIM 18 toolkit for building simulation models, go here Current version: 2.74 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. Analyses include: Reconstruction of ancestral states (parsimony, likelihood) Tests of process of character evolution, including correlation Analysis of speciation and extinction rates Simulation of character evolution (categorical, DNA, continuous) Parametric bootstrapping (integration with programs such as PAUP* and NONA) Morphometrics (PCA, CVA, geometric morphometrics) Coalescence (simulations, other calculations)

94. Clann::: Supertree Software Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees. http://bioinf.may.ie/software/clann/

Clann::: Supertree Software bioinf@nuim clann download tutorial ... Contact Us What is Clann? Clann (the Irish word for "family"), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees. Where has Clann been described? Creevey C. J. and McInerney, J. O. 2005 Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3): 390-2. pdf Creevey C.J., Fitzpatrick DA, Philip GK, Kinsella RJ, O'connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. 2004 Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc R Soc Lond B Biol Sci. 271(1557):2551-8. pdf Where else have we used Clann? Philip, G.K., Creevey, C.J. and McInerney, J.O. (2005). The Opisthokonta and the Ecdysozoa may not be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa. Molecular Biology and Evolution 22, 1175-1184. pdf Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2006). Genome Phylogenies Indicate a Meaningful alpha-Proteobacterial Phylogeny and Support A Grouping of the Mitochondria With the Rickettsiales. Molecular Biology and Evolution

95. 3I - Internet-accessible Interactive Identification Program to create internet-accessible interactive taxonomic keys. http://ctap.inhs.uiuc.edu/dmitriev/

96. R8s_home.htm Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees. http://loco.biosci.arizona.edu/r8s/

r8s version Analysis of rates ("r8s") of evolution programmed by Mike Sanderson Section of Evolution and Ecology UC Davis, Davis CA 95616 May 16, 2006 Introduction The program reads "NEXUS" formatted data (ASCII) files, the standard used by PAUP, MacClade, Component and some other phylogenetic programs (Maddison et al. 1997). This version fixes some minor bugs and compilation problems on various platforms This version improves the robustness of the previous implementation of divergence time estimation routines and adds some entirely new features. The former is achieved by a new and stringent check on solutions via the checkgradient command. In conjunction with the use of multiple replicates from different initial conditions, this is the best line of defense against incorrect results. A new penalty function that penalizes differences in the logarithm of rates on neighboring branches has been added because of occasional pathological behavior of deep time estimates from shallow calibrations When multiple fossil calibrations or constraints are present, a fossil cross-validation procedure can now be invoked (as an option in the divtime command) to undertake model selection using penalized likelihood. This essentially uses the internal consistency among the fossil ages to help select the appropriate level of rate smoothing, and it can also provide a useful estimate of the age errors implied by that level of smoothing. A new likelihood ratio based relative rate test has been added to permit inferences about local shifts in rates of evolution. It has all the advantages (or disadvantages) of other aspects of the program, such as using multiple calibrations or age constraints.

97. Biodiversity Database Management Solutions Database management system for managing data about taxa, species, genera, varieties and cultivars. http://ds.dial.pipex.com/town/square/fd95/

Alice Software News Products Services Information Who are we? We have more than 40 years combined experience in project management and the delivery of information management solutions with a focus on biodiversity, natural resources, conservation, ethno-botany and plant genetic resources. What we offer We help organisations and individuals with an interest in bio-diversity to de fine their knowledge and information management needs and we specify and supply appropriate IT solutions. We work with organisations and individuals to implement strategies for managing biodiversity data. We facilitate or lead project planning and project management using industry standard methods to gather and analyse requirements and to present business and technical options for meeting requirements. We are the creators of the Alice System, a set of database tools for managing biodiversity data. The Alice System can be used to construct a framework, based upon a taxonomy understandable to biologists, for building rich data content knowledgebase s . The tool set can be used to create and publish a wide variety of databases of diverse content including monographic databases, species inventories, annotated checklists or identification keys. The tool set comprises comprises software for data capture and analysis, report generation, web publication (e-publication) and data export into a variety of formats use

98. PaleoTax The program can give an overview of taxonomic and other information of a taxa group. Recorded data can be assessed or exported as RTF or HTML document. http://www.paleotax.de

PaleoTax Database system for Palaeontologists and Biologists Home Download Information F.A.Q. 2.0 (German) Tour (2.1) User What's new ? F.A.Q. 2.1/2.2 (English) PaleoTax/ Map Manual Version 2.3 What is PaleoTax ? PaleoTax is a database management system to record taxonomic, geographic and stratigraphic data in biology and palaeontology and dedicated to taxonomists. PaleoTax may give a complete overview on the literature, taxa, localities, stratigraphy, material etc. of one field of research (as a family, an order or a phylum). Instead taking data from the literature, sample data or field observations can be recorded. With PaleoTax , recorded data can be assessed or exported as RTF or HTML document. The program is available for free since August 2001 in a German and English (from 2009 on also in a Spanish) version for the Windows World. More ... view detailed information on the program (including tour), News , Updates, Service Releases, Get in contact to users and their applications (with examples of databases in the Internet), free Download of the program

99. Bio-Tools.Net TAXIS - Taxonomic Information System - ONE Program To Manage ALL Y Database management system for recording taxa, specimens, characters, and images. Also serves as an interactive identification system. http://www.bio-tools.net/

Bio-Tools.Net TAXIS 3.5 Home Register Download Databases ... FAQ PDF manual Online help Get a FREE copy What's new in TAXIS 3.5 Newsletter: Name: E-mail: Bio-Tools.Net TAXIS 3.5 has been discontinued. TAXIS is not supported and not developed any more. Use it at your own risk. It is kept online primarily for support of existing projects. EarthCape is our next project that is under development. Check out EarthCape web site for more information. Arrange your taxonomic data in a hierarchic tree , create distribution maps with full-featured, built-in GIS , view samples images references characters , and synonyms Manage your specimen collection linked to Taxa and Localities. Map the point-locations in GIS dynamically. Design and print LABELS . Assign images to any record. Build your own identification system by recording characters, linking them to taxa and images. Characters and states are arranged in flexible hierarchical tree. Interactive, multi-entry identification system based on characters, taxa, and images recorded in other sections. Identification branching control allows quick navigation.

100. Identification System PICKEY An interactive multi-entry polychotomous key for identification of organisms by intensive use of images. http://www.zin.ru/projects/pickey

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