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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:  Skillsets

Tree of Life Web Project The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). Each page contains information about a particular group, e.g., salamanders, segmented worms, phlox flowers, tyrannosaurs, euglenids, Heliconius butterflies, club fungi, or the vampire squid. ToL pages are linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things.

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

How-to (GoogleSites) - ePortfolios with GoogleApps developed by Helen C. Barrett, Ph.D. Keeping a Learning Journal The Announcements page type can be used as a form of "blog" or learning journal (sometimes called a learning portfolio), since it allows individual posts, and it is organized in reverse chronological order. The learner can also attach documents to any entry, or can create a link to any GoogleDocs Document/Presentation/Spreadsheet, to another GoogleSites page, or any web page. Create a New Page with Announcements page type.Create a New Post for each entry, to reflect on learning that takes place over time.Use the Insert -> Recent posts Gadget on any page to show a summary of the last few entries (you can indicate the number) -- recommend placing on Home page. At a certain point in time (prior to a parent conference, end of the school year, etc.), a more formal presentation portfolio would be developed, which is discussed below. Authoring an electronic portfolio Create a first page - Introduction & Table of Contents Link to a page

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

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

Students don't pursue STEM because it's too hard, say 52% of Americans When Americans are asked why more students don’t pursue a degree in science, technology, engineering or math (STEM), they are most likely to point to the difficulty of these subjects, according to a new Pew Research Center survey. About half of adults (52%) say the main reason young people don’t pursue STEM degrees is they think these subjects are too hard. Policymakers and educators have long puzzled over why more students do not pursue STEM majors in college, even though those who have an undergraduate degree in a STEM field of study earn more than those with other college majors – regardless of whether they work in a STEM job or a different occupation. Yet only a third of workers (33%) ages 25 and older with at least a bachelor’s degree have an undergraduate degree in a STEM field, according to a new Pew Research Center analysis. Only 13% of the U.S. workforce was employed in STEM occupations as of 2016, while the vast majority (87%) was employed in other occupations.

CIRCOS Circular Genome Data Visualization 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.

The Weird Strategy Dr. Seuss Used to Create His Greatest Work (And Why You Should Use It Too) In 1960, two men made a bet. There was only $50 on the line, but millions of people would feel the impact of this little wager. The first man, Bennett Cerf, was the founder of the publishing firm, Random House. The second man was named Theo Geisel, but you probably know him as Dr. Seuss. Dr. At first glance, you might think this was a lucky fluke. Before we talk about how to get started, though, I wanted to let you know I researched and compiled science-backed ways to stick to good habits and stop procrastinating. Here's what we can learn from Dr. The Power of Constraints What Dr. Setting limits for yourself — whether that involves the time you have to work out, the money you have to start a business, or the number of words you can use in a book — often delivers better results than “keeping your options open.” In fact, Dr. In my experience, I've seen that constraints can also provide benefits in health, business, and life in general. 1. Limitations drive you to figure out solutions. 2.

Web TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but are only available to the authors, publication editors, or reviewers using a special access code. TreeBASE is produced and governed by the The Phyloinformatics Research Foundation, Inc. Some recent additions: <a href=" The current release includes a host of new features and improvements over the previous TreeBASE prototype.

Biology Labs - - Virtual laboratory simulations for science education Below is a list of freely available online biology lab resources, including microscopy, genetics and life science. General biology and virtual labs The Interactive Library – This site is a list of links to interactive biology sites. Anatomy, physiology and dissection See the list of Anatomy Labs Microscopy, cells and microbiology Genetics and DNA Health, medical treatment and blood types Interactive Health Tutorials – From U.S. Population biology and dynamics Animal behavior, evolution and life science The Animal Behavior Project – At the University of ArizonaLife Science – Interactive lessons from learningscience.comShedd Educational Adventures – Marine life resources from the Shed AquariumPaleo Pursuit – A game from The Virtual Museum of CanadaENSI/SENSI – Evolution and the Nature of Science InstitutesIlluminating Photosynthesis – PBS interactive tutorial about photosynthesis; not a lab activity Commercial products Return to the List of Subjects.

Stanford psychology expert: The No. 1 work skill of the future It’s 9 a.m.: You walk into the office, sit down, fire up your computer and attempt to start your workday. Ping! Everyone is talking about Trump’s latest tweet. You pick up your phone to look at the news notification and answer your text, only to check a Facebook post and then watch a Youtube video. A lack of focus comes at a cost The challenge at work, of course, has always been to dodge things that distract us. The amount of information available, the speed at which it can be disseminated and the ubiquity of access to new content on our devices has made for a trifecta of distraction. What’s the cost of all this? That was true decades ago, but it’s truer than ever today. The most important skill of the 21st century The workplace is rapidly changing, and in the near future, there will be two kinds of people in the world: those who let their attention and lives be controlled and coerced by others and those who proudly call themselves “indistractable.” Email Group chats Meetings Your phone

PhyloPic — Free Silhouette Images of Life Forms