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
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.
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
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
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?
Why Phone Conversations Are Better Than Texting Nevertheless, I’m here today to confess my sins and ask forgiveness from all those whose voicemails I have not listened to. To fully repent, I must make clear what I now know to be the truth: Phone calls are good, actually. One of the best arguments in favor of phone calls will be obvious to anyone who’s ever gone back and forth for three days via email trying to pick a spot for Tuesday’s happy hour. Guhan Subramanian, the director of the Harvard Program on Negotiation, which teaches business- and law-school students the finer points of conflict resolution, argues that spoken conversation accomplishes far more in a shorter amount of time. This difference is what first pushed me back to phone calls. With so many digital avenues now available for reaching someone, the problem with phone calls is not that they’re inconvenient. I’m not advocating a wholesale rejection of texting in favor of speaking. But that itself can come with some drawbacks, according to Subramanian.
How To Stop Checking Your Phone: 4 Secrets From Research Before we commence with the festivities, I wanted to thank everyone for helping my first book become a Wall Street Journal bestseller. To check it out, click here. If I told you we check our phones 5 billion times a minute you’d probably just shrug and agree. Here’s what NYU professor Adam Alter told me: There’s a study that was done asking people, mainly young adults, to make a decision: if you had to break a bone or break your phone what would you prefer? May I suggest that this has finally gotten out of hand? We’re not looking at the problem correctly. You do not have a short attention span. Have you had multiple car crashes this week because you can’t pay attention to the road? See? That’s not a short attention span. This thing you call “your life” is made of memories. These days we spend so much time trying to get others attention yet the true determinant of our happiness is where we direct our own. We have a “mind control” problem. So what do we do? Nah. Good. Well, I lied. Sum Up
Are we losing the art of telephone conversation? | Zoe Williams Statistics illustrating our addiction to our smartphones come out quite frequently and receive a lot of attention for information so unsurprising; it will come as no shock to anyone that the average Briton checks her phone every 12 minutes. Indeed, I’d like to pick a fight with the blandness of the questions asked in Ofcom’s latest telecommunications report. I wish they’d included: “Have you ever picked up your phone to Google where your phone is?” Or: “Have you ever smashed or otherwise been suddenly deprived of your phone, and wanted to stand in the street howling like a wolf?” The report belongs in the news category “things we already knew, but are worried about, so will continue to pick at like a scab”. Digital natives probably wouldn’t understand a phone call of the olden days; meandering, one-on-one, hours long. The other great disincentive is the voicemail: there’s nobody left on Earth who listens to them, but everyone has a recorded message insisting that they will.
ePortfolio Tools | ePortfolio Review Please add and review the eportfolio system you use at your school, college or university. Below is a list of the eportfolios we are reviewing along with others we felt were worth noting. Please comment on the eportfolio platforms and make suggestions for others we should review. Please indicate which eportfolio category (categories) best suit the eportfolio platform you are reviewing…Showcase, Learning, Career and Course/Program Assessment. Epsilen Showcase eportfolio – no charge Epsilen Environment is the result of six years of research and development at the Purdue School of Engineering and Technology at Indiana University Purdue University Indianapolis (IUPUI). Like this: Like Loading...