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Phylogeny Programs

Here are 392 phylogeny packages and 54 free web servers, (almost) all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly monthly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines. The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses. ... by methods available ... by computer systems on which they work ... cross-referenced by method and by computer system. ... by ones which analyze particular kinds of data. Related:  Mind Maps/Thinking Maps/Graphic Organizers

Tree of Life Explorer View your own data online Note that your data is only stored on your personal computer for this visualisation and is not transmitted over the internet so it is safe to visualise unpublished data in this way. If you prefer, you can still download OneZoom and do everyting locally and offline. Click here to load the single stand alone file version of OneZoom in a new window. This code is a slightly updated version of the supplementary material to the article in PLoS Biology. The code is also available for download as a zip in the downloads section of this page. Now you are exploring your tree in OneZoom. Downloads and source code Download the single stand alone file version of OneZoom with embedded data in a zip file mammals , bacteria , birds , amphibians Download the open source OneZoom code with embedded data in a zip file mammals , birds , amphibians , tetrapods . Download the paper here. More trees on OneZoom Please see the main page for links to most of our trees. Zanne et. al.

Phylogenetic Analysis by Maximum Likelihood (PAML) Ziheng Yang Table of contents Introduction PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. This document is about downloading and compiling PAML and getting started. Downloading and Setting up PAML PAML-X: A GUI for PAML A graphical user interface, called PAML-X, has been written by Bo Xu of Institute of Zoology, Chinese Academy of Sciences in Beijing. The following is written for the naive user. PAML for Windows 9x/NT/2000/XP/Vista/7 Download and save the archive paml4.7a.tgz or paml4.8.tgz, on your local disk (Make sure you save the file using the correct name. Setting up a folder of local programs and changing the search path. Next we will add this folder onto the search path, which the OS uses to search for executable programs. Copy the PAML executables. You can also copy other command-line programs you downloaded into this folder, such as mb, RAxML, PhyML programs. Running a PAML program. C: cd \Programs\paml4.7a\ codeml

Softwares list UWashington This list is by no means complete or even exhaustive. At the bottom of the page, there are some other lists you may want to consult. New programs appear almost monthly (most published in Molecular Ecology Resources), so stay aware of developments in the field. General Purpose Programs These programs are a collection of tests and methods commonly used in population genetics Arlequin General purpose package that does almost every analysis in the book, and accepts microsatellite, allozyme, sequence and other data. PowerMarker Potentially powerful program that calculates all sorts of genetic distances and also does a few other things that no other program does. Genetix Powerful analysis package for population genetics, but you have to understand French. Estimation and Test of Population Genetic Parameters performs exact tests for deviation from Hardy-Weinberg, linkage disequilibrium, population differentiation and isolation by distance (DOS). ChiFish PowSim RSTCalc Spagedi Microchecker Pedant Migrate

OneZoom Tree of Life Explorer Inciter les élèves à construire une carte | HeuristicFLE Si vous souhaitez que vos élèves réalisent une carte alors qu’ils n’en ont jamais fait, il y a une manière très simple de s’y prendre : Il suffit de les accompagner dans la construction de la carte en travaillant en groupe, puis individuellement. Ainsi on permet aux élèves de découvrir l’outil tout en en faisant l’expérience. Il est inutile de parler de "carte heuristique" ou de "carte mentale" avant de commencer. Imaginons que vous travailliez sur le thème "Etrange étranger" du livret "Visions de l’autre" (chp2) 1-Produire des idées Dans un premier temps, inscrivez au tableau le thème en grand et entourez-le d’un petit nuage (ou mur s’il est lisse en écrivant le thème sur une feuille A4).Puis, distribuer des post-it aux élèves.Annoncer le sujet et demandez-leur d’écrire les mots que leur évoquent "Etrange étranger". 2-Réunir ce qui est épars Ils devront ensuite se lever et venir "coller" leurs idées tout autour, sans souci d’ordre ou de hiérarchie. 3-Thématiser et regrouper l’info Like this:

TREE-PUZZLE Phylogenetics Softwares list (Taxonomy Zoology UK) This is a list of some taxonomic and phylogenetic software, with emphasis on tree building and molecular data. There are also links to other, more extensive collections that may have what you're looking for if you can't find it here. Contents Tree viewing Tree building Tree comparison and interpretation Sequence format converters Sequence alignment, analysis, and searching RNA secondary structure Software archives Tree viewing TreeView View NEXUS and PHYLIP format tree files on Macs (68K and Power Mac) and Windows (16 and 32 bit). TreeExplorer View and manipulate MEGA format trees under Windows. Tree building Collection of APL Functions for Cladistic Analysis, written by Rino Zandee. Standard program for phylogenetic analysis (currently Macintosh only but PAUP* for PowerMac, DOS, and Unix is coming). The most comphrehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood, and distance methods, plus utility programs. U.K. mirror site for PHYLIP Spectrum TreeMap

StratomeX — Institute for Computer Graphics and Vision Demonstration Video of Caleydo StratomeX Caleydo StratomeX is a visualization technique for the analysis of multiple stratified datasets. A good example for such an analysis scenario is the identification and characterization of cancer subtypes. Understanding subtypes is a precondition for refined therapeutic targeting which in turn is an important step towards improved patient outcomes. Recent research has shown that integrated analysis of different molecular data types generated by the TCGA project can be used to discover subtypes and suggest molecular differences relevant for therapeutic approaches. StratomeX can be used to explore the results of data analysis systems developed to perform analyses of TCGA data. StratomeX makes such analysis results easier accessible and requires no scripting. The core concept of our approach is to visualize stratifications (groupings) of samples (patients) and the relationships between these groupings in a given cancer type. Examples Donwload Help

The Method - Information Mapping Information Mapping® is a research-based method used to analyze, organize and present information based on your audience’s needs and the purpose of the information. Introduction video Organizational challenges Poorly written documentation, training, memos, reports and emails can cause significant problems for organizations. Reader and writer challenges Writers and readers of business communications are faced with these challenges: Large amounts of complex or technical informationToo much or too little detailCritical information is buried and hard to findLack of organization and logical structure Our solution Information Mapping overcomes these challenges. Read more...

MrBayes: Home Population Genomics and Bioinformatics - Population Genetics Visualization Tools I would like to share a list of tools that visualize population genetics processes. First, let me share an amazing story from John Turner, Emeritus Prof. of Univ. of Leeds about tools that visualize evolution. This story took place in 1968 in University of York: "My compliments on your putting up that compilation on the web. Many thanks to the Evoldir members who provided the information: Andres J. For some tools I post information found in their webpages Populus The Populus software contains a set of simulations that we use to teach population biology and evolutionary ecology at the University of Minnesota. CIRCOS Circular Genome Data Visualization Infographic: 14 best practices for advanced mind maps Jul 25th, 2013 | By Chuck Frey | Category: Resources So you’ve invested in mind mapping software and have created some basic visual diagrams with it. What’s next? You need to learn how to use its more advanced capabilities, because they’re the key to getting the majority of of the business value out of it. This infographic (click on the image above to view the full version) summarizes 14 best practices for utilizing the deep capabilities of mind mapping software – from tasks and linked documents to callouts and boundaries, knowing how to use these elements correctly is critically important, especially if you plan to share your mind maps with others. Download this diagram as a PDF file View it as a large format PNG image View it on Pinterest Want to learn more? For more details on the elements of mind maps and how to use them effectively, please visit my Elements of Effective Mind Maps How-to Guide, a collection of blog posts that goes into much greater depth on each of these topics.