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
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.
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
Catalogue of Organisms: Where To Next? As some of you may have noticed over the course of the past year, I have an interest in phylogenetically problematic taxa. I think anyone with even a passing interest in evolutionary matters does: few things appeal to the human spirit more than a good mystery. So I've decided to give you my own completely-biased, not-in-the-least-bit-impartial list of the ten taxa that I think currently spark the most phylogenetic questions, based on nothing more than my own subjective judgement. The mitrate Rhenocystis latipedunculata. Photo from The Virtual Fossil Museum. 1 - Stylophora: These featured here a couple of weeks ago. Photo by Linda de Volder. 2 - Opisthocomus hoazin: The hoatzin, the prime exemplar of all things uncertain in avian systematics. The pycnogonid Nymphon gracile. 3 - Pycnogonida: The sea-spiders, bizarre marine organisms that appear all legs and only barely arthropod. The palpigrade Eukoenenia mirabilis. The flying duck orchid (Caleana major). Galapagos tortoises. Rieger, R.
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
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.
Ethnoecology Ethnoecology is the scientific study of how different groups of people living in different locations understand the ecosystems around them, and their relationships with surrounding environments. It seeks valid, reliable understanding of how we as humans have interacted with the environment and how these intricate relationships have been sustained over time. The "ethno" (see ethnology) prefix in ethnoecology indicates a localized study of a people, and in conjunction with ecology, signifies people's understanding and experience of environments around them. Ecology is the study of the interactions between living organisms and their environment; enthnoecology applies a human focused approach to this subject. The development of the field lies in applying indigenous knowledge of botany and placing it in a global context. History Ethnoecology began with some of the early works of Dr. Principles Traditional ecological knowledge Local knowledge in western society
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