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
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 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[edit] Ethnoecology began with some of the early works of Dr. Principles[edit] Traditional ecological knowledge[edit] Local knowledge in western society[edit]
MrBayes: Home 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. 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. If you’re five foot five inches tall and you’re playing basketball, you figure out more creative ways to score than the six foot five inch guy. Limitations drive you to figure out solutions. 2. Constraints are Not the Enemy
Journal of Ethnobiology and Ethnomedicine | Home page NJplot NEW: NJplot plots trees in PDF and PostScript formats (not for MacOS). NEW: NJplot allows to open several tree windows. NEW: NJplot can draw multibranched trees with or without branch lengths. NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). A screen shot of the main window of njplot is available here. Use of NJPlot Any rooting of the unrooted tree can be interactively specified using the mouse. Download NJplot Executables and full source code can be downloaded through our FTP server. The Mac and Windows versions are self-extracting archives which include an example file, help information, and the unrooted program that draws unrooted trees. For unix versions, get also an example tree file and the on-line help file. Use as a helper application NJplot can be used as a standalone application or as a helper application when using the World Wide Web. Reference
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
Attention “Blinks” Differently for Plants and Animals How to tell if you’re being ‘breadcrumbed’ at work - BBC Worklife Stop breadcrumbing me! Our modern dating vocabulary is making its way into our work lexicon, and it’s bringing more life and colour to the way we describe our experiences. Have you ever been ghosted by a potential employer? Or have you ghosted them? Now, thanks to the latest series of the reality TV show Love Island, we have a new word for an old practice: breadcrumbing. “Breadcrumbing is when you leave little bits of bread for someone. Whether you’re being strung along in a drawn-out hiring process or your existing employer is leading you on, breadcrumbing gives you “just enough” to keep you on the line. “Breadcrumbing is really a modern term for what we used to call intermittent reinforcement, which is one of the strongest ways to develop someone's behaviour,” says B Lynn Ware, an industrial/organisational psychologist and the CEO of a leadership consultancy in California. But what if they’re not actually using it for employee development?