Recent Changes for "2008 Workshop" - Bodega Phylogenetics Wikihttp://bodegaphylo.wikispot.org/2008_WorkshopRecent Changes of the page "2008 Workshop" on Bodega Phylogenetics Wiki.en-us 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-20 07:13:13glor <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 15: </td> <td> Line 15: </td> </tr> <tr> <td> <span>-</span> ||Balinda||Sheila||Makerere U||[[MailTo(Sbalinda AT muienr DOT mak DOT ac DOT ug)]]||<br> <span>-</span> ||Bess||Emilie||Illinois||[[MailTo(bess AT inhs DOT uiuc DOT edu)]]||<br> <span>-</span> ||Clucas||Barbara||UCD||[[MailTo(baclucas AT ucdavis DOT edu)]]||<br> <span>- ||Drauch||Andrea</span>||UCD||[[MailTo(amdrauch AT ucdavis DOT edu)]]||<br> <span>-</span> ||Finger||Amanda||UCD||[[MailTo(ajfinger AT ucdavis DOT edu)]]||<br> <span>-</span> ||Glass||Jennifer||Arizona State||[[MailTo(jbglass1 AT asu DOT edu)]]||<br> <span>-</span> ||Greenberg||Anne||Yale||[[MailTo(anne DOT greenberg AT yale DOT edu)]]||<br> <span>-</span> ||Grossenbacher||Dena||UCD||[[MailTo(dgrossenbacher AT ucdavis DOT edu)]]||<br> <span>-</span> ||Grusz||Amanda||Duke||[[MailTo(alg3 AT duke DOT edu)]]||<br> <span>-</span> ||Hornsby||Angela||Idaho State||[[MailTo(adhornsby AT gmail DOT com)]]||<br> <span>-</span> ||Krakos||Kyra||WUSTL||[[MailTo(knburras AT artsci DOT wustl DOT edu)]]||<br> <span>-</span> ||Kurushima||Jennifer||UCD||[[MailTo(jdkurushima AT ucdavis DOT edu)]]||<br> <span>-</span> ||Long||Elizabeth||UCD||[[MailTo(eclong AT ucdavis DOT edu)]]||<br> <span>-</span> ||Pennington||Jillian||Yale||[[MailTo(jillian DOT pennington AT yale DOT edu)]]||<br> <span>-</span> ||Robertson||Kelly||U Illinois||[[MailTo(krober6 AT uic DOT edu)]]||<br> <span>-</span> ||Robinson||Donelle||Ohio U||[[MailTo(dr647706 AT ohio DOT edu)]]||<br> <span>-</span> ||Schirtzinger||Erin||New Mexico State||[[MailTo(eesem AT nmsu DOT edu)]]||<br> <span>-</span> ||van Herwerden||Lynne||James Cook||[[MailTo(lynne DOT vanherwerden AT jcu DOT edu DOT au)]]||<br> <span>-</span> ||Anacker||Brian||UCD||[[MailTo(blanacker AT ucdavis DOT edu)]]||<br> <span>-</span> ||Beaulieu||Jeremy||Yale||[[MailTo(jeremy DOT beaulieu AT yale DOT edu)]]||<br> <span>-</span> ||Bloom||Devin||U Toronto||[[MailTo(devin DOT bloom AT utoronto DOT ca)]]||<br> <span>-</span> ||Busch||Joseph||Purdue||[[MailTo(jdbusch AT purdue DOT edu)]]||<br> <span>-</span> ||Camargo||Arley||BYU||[[MailTo(arley_camargo AT byu DOT net)]]||<br> <span>-</span> ||Diogo||Rui||GW||[[MailTo(ruidiogo AT gwu DOT edu)]]||<br> <span>-</span> ||Doffitt||Chris||MS State||[[MailTo(chd19 AT msstate DOT edu)]]||<br> <span>-</span> ||Ellingson||Ryan||UCLA||[[MailTo(rellingson AT ucla DOT edu)]]||<br> <span>-</span> ||Hansen||Daniel||Denmark Tech||[[MailTo(daniel AT cbs DOT dtu DOT dk)]]||<br> <span>-</span> ||Muir||Chris||Indiana<span>||[[MailTo(cdmuir AT indiana DOT edu)]]||<br> -</span> ||Pearse||Ian||UCD||[[MailTo(ispearse AT ucdavis DOT edu)]]||<br> <span>-</span> ||Pightling||Arthur||U Iowa||[[MailTo(arthur-pightling AT uiowa DOT edu)]]||<br> <span>-</span> ||Piwczynski||Marcin||Copernicus U||[[MailTo(piwczyn AT umk DOT pl)]]||<br> <span>-</span> ||Rejmanek||Daniel||UCD||[[MailTo(drejmanek AT ucdavis DOT edu)]]||<br> <span>-</span> ||Sangula||Abraham||Makerere U||[[MailTo(aksangula AT muienr DOT mak DOT ac DOT ug)]]||<br> <span>-</span> ||Sedano||Raul||UCLA||[[MailTo(rsedano AT ucla DOT edu)]]||<br> <span>-</span> ||Sedio||Brian||Michigan||[[MailTo(bsedio AT umich DOT edu)]]||<br> <span>-</span> ||Wolfe||Benjamin||Harvard||[[MailTo(bewolfe AT fas DOT harvard DOT edu)]]|| </td> <td> <span>+</span> ||Balinda||Sheila||<span>Uganda||</span>Makerere U||[[MailTo(Sbalinda AT muienr DOT mak DOT ac DOT ug)]]||<br> <span>+</span> ||Bess||Emilie||<span>USA||</span>Illinois||[[MailTo(bess AT inhs DOT uiuc DOT edu)]]||<br> <span>+</span> ||Clucas||Barbara||U<span>SA||U</span>CD||[[MailTo(baclucas AT ucdavis DOT edu)]]||<br> <span>+ ||Drauch||Andrea||USA</span>||UCD||[[MailTo(amdrauch AT ucdavis DOT edu)]]||<br> <span>+</span> ||Finger||Amanda<span>||USA</span>||UCD||[[MailTo(ajfinger AT ucdavis DOT edu)]]||<br> <span>+</span> ||Glass||Jennifer<span>||USA</span>||Arizona State||[[MailTo(jbglass1 AT asu DOT edu)]]||<br> <span>+</span> ||Greenberg||Anne||<span>USA||</span>Yale||[[MailTo(anne DOT greenberg AT yale DOT edu)]]||<br> <span>+</span> ||Grossenbacher||Dena||U<span>SA||U</span>CD||[[MailTo(dgrossenbacher AT ucdavis DOT edu)]]||<br> <span>+</span> ||Grusz||Amanda||<span>USA||</span>Duke||[[MailTo(alg3 AT duke DOT edu)]]||<br> <span>+</span> ||Hornsby||Angela||<span>USA||</span>Idaho State||[[MailTo(adhornsby AT gmail DOT com)]]||<br> <span>+</span> ||Krakos||Kyra||<span>USA||</span>WUSTL||[[MailTo(knburras AT artsci DOT wustl DOT edu)]]||<br> <span>+</span> ||Kurushima||Jennifer||U<span>SA||U</span>CD||[[MailTo(jdkurushima AT ucdavis DOT edu)]]||<br> <span>+</span> ||Long||Elizabeth||U<span>SA||U</span>CD||[[MailTo(eclong AT ucdavis DOT edu)]]||<br> <span>+</span> ||Pennington||Jillian||<span>USA||</span>Yale||[[MailTo(jillian DOT pennington AT yale DOT edu)]]||<br> <span>+</span> ||Robertson||Kelly||U<span>SA||U</span> Illinois||[[MailTo(krober6 AT uic DOT edu)]]||<br> <span>+</span> ||Robinson||Donelle<span>||USA</span>||Ohio U||[[MailTo(dr647706 AT ohio DOT edu)]]||<br> <span>+</span> ||Schirtzinger||Erin||<span>USA||</span>New Mexico State||[[MailTo(eesem AT nmsu DOT edu)]]||<br> <span>+</span> ||van Herwerden||Lynne||<span>Australia||</span>James Cook||[[MailTo(lynne DOT vanherwerden AT jcu DOT edu DOT au)]]||<br> <span>+</span> ||Anacker||Brian||U<span>SA||U</span>CD||[[MailTo(blanacker AT ucdavis DOT edu)]]||<br> <span>+</span> ||Beaulieu||Jeremy||<span>USA||</span>Yale||[[MailTo(jeremy DOT beaulieu AT yale DOT edu)]]||<br> <span>+</span> ||Bloom||Devin||<span>Canada||</span>U Toronto||[[MailTo(devin DOT bloom AT utoronto DOT ca)]]||<br> <span>+</span> ||Busch||Joseph||<span>USA||</span>Purdue||[[MailTo(jdbusch AT purdue DOT edu)]]||<br> <span>+</span> ||Camargo||Arley<span>||USA</span>||BYU||[[MailTo(arley_camargo AT byu DOT net)]]||<br> <span>+</span> ||Diogo||Rui<span>||USA</span>||GW||[[MailTo(ruidiogo AT gwu DOT edu)]]||<br> <span>+</span> ||Doffitt||Chris||<span>USA||</span>MS State||[[MailTo(chd19 AT msstate DOT edu)]]||<br> <span>+</span> ||Ellingson||Ryan||U<span>SA||U</span>CLA||[[MailTo(rellingson AT ucla DOT edu)]]||<br> <span>+</span> ||Hansen||Daniel||Denmark<span>||Denmark</span> Tech||[[MailTo(daniel AT cbs DOT dtu DOT dk)]]||<br> <span>+</span> ||Muir||Chris||<span>USA||</span>Indiana<span>&nbsp;University||[[MailTo(cdmuir AT indiana DOT edu)]]||<br> +</span> ||Pearse||Ian||U<span>SA||U</span>CD||[[MailTo(ispearse AT ucdavis DOT edu)]]||<br> <span>+</span> ||Pightling||Arthur<span>||USA</span>||U Iowa||[[MailTo(arthur-pightling AT uiowa DOT edu)]]||<br> <span>+</span> ||Piwczynski||Marcin||<span>Poland||</span>Copernicus U||[[MailTo(piwczyn AT umk DOT pl)]]||<br> <span>+</span> ||Rejmanek||Daniel||U<span>SA||U</span>CD||[[MailTo(drejmanek AT ucdavis DOT edu)]]||<br> <span>+</span> ||Sangula||Abraham||<span>Uganda||</span>Makerere U||[[MailTo(aksangula AT muienr DOT mak DOT ac DOT ug)]]||<br> <span>+</span> ||Sedano||Raul<span>||USA</span>||UCLA||[[MailTo(rsedano AT ucla DOT edu)]]||<br> <span>+</span> ||Sedio||Brian||<span>USA||</span>Michigan||[[MailTo(bsedio AT umich DOT edu)]]||<br> <span>+</span> ||Wolfe||Benjamin||<span>USA||</span>Harvard||[[MailTo(bewolfe AT fas DOT harvard DOT edu)]]|| </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 11:56:06BobThomsonadding student list <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 12: </td> <td> Line 12: </td> </tr> <tr> <td> </td> <td> <span>+ <br> + =Students=<br> + <br> + ||Balinda||Sheila||Makerere U||[[MailTo(Sbalinda AT muienr DOT mak DOT ac DOT ug)]]||<br> + ||Bess||Emilie||Illinois||[[MailTo(bess AT inhs DOT uiuc DOT edu)]]||<br> + ||Clucas||Barbara||UCD||[[MailTo(baclucas AT ucdavis DOT edu)]]||<br> + ||Drauch||Andrea||UCD||[[MailTo(amdrauch AT ucdavis DOT edu)]]||<br> + ||Finger||Amanda||UCD||[[MailTo(ajfinger AT ucdavis DOT edu)]]||<br> + ||Glass||Jennifer||Arizona State||[[MailTo(jbglass1 AT asu DOT edu)]]||<br> + ||Greenberg||Anne||Yale||[[MailTo(anne DOT greenberg AT yale DOT edu)]]||<br> + ||Grossenbacher||Dena||UCD||[[MailTo(dgrossenbacher AT ucdavis DOT edu)]]||<br> + ||Grusz||Amanda||Duke||[[MailTo(alg3 AT duke DOT edu)]]||<br> + ||Hornsby||Angela||Idaho State||[[MailTo(adhornsby AT gmail DOT com)]]||<br> + ||Krakos||Kyra||WUSTL||[[MailTo(knburras AT artsci DOT wustl DOT edu)]]||<br> + ||Kurushima||Jennifer||UCD||[[MailTo(jdkurushima AT ucdavis DOT edu)]]||<br> + ||Long||Elizabeth||UCD||[[MailTo(eclong AT ucdavis DOT edu)]]||<br> + ||Pennington||Jillian||Yale||[[MailTo(jillian DOT pennington AT yale DOT edu)]]||<br> + ||Robertson||Kelly||U Illinois||[[MailTo(krober6 AT uic DOT edu)]]||<br> + ||Robinson||Donelle||Ohio U||[[MailTo(dr647706 AT ohio DOT edu)]]||<br> + ||Schirtzinger||Erin||New Mexico State||[[MailTo(eesem AT nmsu DOT edu)]]||<br> + ||van Herwerden||Lynne||James Cook||[[MailTo(lynne DOT vanherwerden AT jcu DOT edu DOT au)]]||<br> + ||Anacker||Brian||UCD||[[MailTo(blanacker AT ucdavis DOT edu)]]||<br> + ||Beaulieu||Jeremy||Yale||[[MailTo(jeremy DOT beaulieu AT yale DOT edu)]]||<br> + ||Bloom||Devin||U Toronto||[[MailTo(devin DOT bloom AT utoronto DOT ca)]]||<br> + ||Busch||Joseph||Purdue||[[MailTo(jdbusch AT purdue DOT edu)]]||<br> + ||Camargo||Arley||BYU||[[MailTo(arley_camargo AT byu DOT net)]]||<br> + ||Diogo||Rui||GW||[[MailTo(ruidiogo AT gwu DOT edu)]]||<br> + ||Doffitt||Chris||MS State||[[MailTo(chd19 AT msstate DOT edu)]]||<br> + ||Ellingson||Ryan||UCLA||[[MailTo(rellingson AT ucla DOT edu)]]||<br> + ||Hansen||Daniel||Denmark Tech||[[MailTo(daniel AT cbs DOT dtu DOT dk)]]||<br> + ||Muir||Chris||Indiana||[[MailTo(cdmuir AT indiana DOT edu)]]||<br> + ||Pearse||Ian||UCD||[[MailTo(ispearse AT ucdavis DOT edu)]]||<br> + ||Pightling||Arthur||U Iowa||[[MailTo(arthur-pightling AT uiowa DOT edu)]]||<br> + ||Piwczynski||Marcin||Copernicus U||[[MailTo(piwczyn AT umk DOT pl)]]||<br> + ||Rejmanek||Daniel||UCD||[[MailTo(drejmanek AT ucdavis DOT edu)]]||<br> + ||Sangula||Abraham||Makerere U||[[MailTo(aksangula AT muienr DOT mak DOT ac DOT ug)]]||<br> + ||Sedano||Raul||UCLA||[[MailTo(rsedano AT ucla DOT edu)]]||<br> + ||Sedio||Brian||Michigan||[[MailTo(bsedio AT umich DOT edu)]]||<br> + ||Wolfe||Benjamin||Harvard||[[MailTo(bewolfe AT fas DOT harvard DOT edu)]]||</span> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 10:07:42BobThomson <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 12: </td> <td> Line 12: </td> </tr> <tr> <td> </td> <td> <span>+ <br> + ["Student Pages"]</span> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 09:34:07BobThomson <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 1: </td> <td> Line 1: </td> </tr> <tr> <td> <span>- The 2008 Workshop recently wrapped up.<br> - </span> </td> <td> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 09:33:51BobThomson <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 1: </td> <td> Line 1: </td> </tr> <tr> <td> <span>- The 2008 Workshop recently wrapped up. We've archived the course schedule and related information and handouts here.<br> - <br> - =2008 Workshop=<br> - [[Image(2008_class_photo.jpg, 700, thumbnail, "2008 Workshop Participants")]]<br> - <br> - [[Image(Bodega_work.jpg,221, thumbnail, "Students working on an exercise")]][[Image(Bodega_lunch.jpg, 222,thumbnail, "Lunch on the lab's patio")]][[Image(Bodega_hike.jpg,221, thumbnail, "Peter Wainwright's annual beach hike")]]<br> - </span> </td> <td> <span>+ The 2008 Workshop recently wrapped up.</span> </td> </tr> <tr> <td> Line 40: </td> <td> Line 34: </td> </tr> <tr> <td> </td> <td> <span>+ =2008 Workshop=<br> + [[Image(2008_class_photo.jpg, 700, thumbnail, "2008 Workshop Participants")]]</span> </td> </tr> <tr> <td> Line 41: </td> <td> Line 37: </td> </tr> <tr> <td> </td> <td> <span>+ [[Image(Bodega_work.jpg,221, thumbnail, "Students working on an exercise")]][[Image(Bodega_lunch.jpg, 222,thumbnail, "Lunch on the lab's patio")]][[Image(Bodega_hike.jpg,221, thumbnail, "Peter Wainwright's annual beach hike")]]</span> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 09:30:53BobThomson <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 1: </td> <td> Line 1: </td> </tr> <tr> <td> <span>- Welcome to the Applied Phylogenetics Wiki! This wiki has grown from a week-long workshop in applied phylogenetics that is held each Spring at the Bodega Bay Marine Lab. The primary goal of the wiki is to provide a forum for instructors and students to share files, datasets, links, and other information. We've elected the wiki format because it is remarkably easy to use; we have inserted a very short guide on how to do common things ["Wiki Quickstart" here]. Virtually everything is edit-able, so feel free to add or change content.<br> - </span> </td> <td> <span>+ The 2008 Workshop recently wrapped up. We've archived the course schedule and related information and handouts here.</span> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-19 09:28:19BobThomsonRenamed from "Front Page" (archiving 2008 workshop to its own page, will make a new front page) <div id="content" class="wikipage content"> Differences for 2008 Workshop<p><strong></strong></p><table> <tr> <td> <span> Deletions are marked with - . </span> </td> <td> <span> Additions are marked with +. </span> </td> </tr> <tr> <td> Line 1: </td> <td> Line 1: </td> </tr> <tr> <td> </td> <td> <span>+ Welcome to the Applied Phylogenetics Wiki! This wiki has grown from a week-long workshop in applied phylogenetics that is held each Spring at the Bodega Bay Marine Lab. The primary goal of the wiki is to provide a forum for instructors and students to share files, datasets, links, and other information. We've elected the wiki format because it is remarkably easy to use; we have inserted a very short guide on how to do common things ["Wiki Quickstart" here]. Virtually everything is edit-able, so feel free to add or change content.<br> + <br> + <br> + =2008 Workshop=<br> + [[Image(2008_class_photo.jpg, 700, thumbnail, "2008 Workshop Participants")]]<br> + <br> + [[Image(Bodega_work.jpg,221, thumbnail, "Students working on an exercise")]][[Image(Bodega_lunch.jpg, 222,thumbnail, "Lunch on the lab's patio")]][[Image(Bodega_hike.jpg,221, thumbnail, "Peter Wainwright's annual beach hike")]]<br> + <br> + <br> + [[anchor(2008 Schedule)]]<br> + =Schedule=<br> + ||&lt;tableborder="1" tablewidth="70%" rowbgcolor="#FFFFE0" align="center"&gt;||'''Morning'''||'''Afternoon'''||'''Evening'''||<br> + ||'''Saturday'''||&lt;#E0E0FF&gt;||Arrivals||Setup ["Student Projects"]||<br> + ||'''Sunday'''||["Phylogenetics Medley"] '''([http://bodegaphylo.wikispot.org/Phylogenetics_Medley?action=Files&amp;do=view&amp;target=EcoPhylo.ppt Wainwright ppt])''' / ["ML phylogenetics tutorial (O'Meara)" PAUP tutorial (O'Meara)] '''([http://bodegaphylo.wikispot.org/ML_phylogenetics_tutorial_%28O%27Meara%29?action=Files&amp;do=view&amp;target=PaupLecture.pdf lecture pdf])'''||["Bayesian Phylogenetics (Rannala)"]||["Phylogeography (Lemmon &amp; Lemmon)"]||<br> + ||'''Monday'''||["Species Concepts (de Queiroz)"]/ ["Tree-Based Species Delimitation (O'Meara)"] ('''[[File(OMearaSpeciesDelimLecture.pdf)]]''')||["Species Boundaries (Shaffer)"] / ["Structurama tutorial (Thomson)"]|| ["Discussion: Rank Free taxonomy (Mishler)"]||<br> + ||'''Tuesday'''||["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstruction.pdf Ancestral_Reconstruction.pdf]'''), '''[http://www.brianomeara.info/BodegaPresentations/Discrete_Character_Correlation.pdf Discrete_Character_Correlation.pdf]''')||["Comparative Methods II (Whittall)"][[File(Whittall ppt.pdf)]]||["Phylogenomics (Eisen)"]/["Web tools for Phylogenetics (Thomson)"]||<br> + ||'''Wednesday'''||["Morphological Diversification (Wainwright &amp; O'Meara)"] ('''[[File(OMearaBrownieLecture.pdf)]]''')||FIELD TRIPS||["NESCent overview (O'Meara)"]/ ["R Tutorial (Glor &amp; O'Meara)"]||<br> + ||'''Thursday'''||["Divergence Times &amp; BEAST tutorial (Moore)"]||["Diversification Rates (Moore)"]||Work on Projects (also a ["Bay Area Biosystematists meeting"])||<br> + ||'''Friday'''||Finish up projects &amp; Begin Presentations||More Student Presentations||Free||<br> + ||'''Saturday'''||Pack up and go home||&lt;#E0E0FF&gt; ||&lt;#E0E0FF&gt; ||<br> + <br> + <br> + =Instructors=<br> + || ||'''Institution'''||'''Topic'''||'''Email'''||<br> + ||Kevin de Queiroz||Smithsonian Institution||Species &amp; Rank Free Taxonomy||[[MailTo(dequeirozk AT si DOT edu)]]||<br> + ||Jonathan Eisen||UC Davis||Phylogenomics||[[MailTo(jaeisen AT ucdavis DOT edu)]]||<br> + ||Rich Glor||University of Rochester||Comparative Methods||[[MailTo(rglor AT mail DOT rochester DOT edu)]]||<br> + ||Alan Lemmon||UC Davis||Phylogeographic Methods||[[MailTo(arlemmon AT ucdavis DOT edu)]]||<br> + ||Brent Mishler||UC Berkeley||Rank Free Taxonomy||[[MailTo(BMishler AT calmail DOT berkeley DOT edu)]]||<br> + ||Brian Moore||UC Berkeley||Species Diversification||[[MailTo(brian DOT moore AT yale DOT edu)]]||<br> + ||Emily Moriarty Lemmon||UC Davis||Phylogeographic Methods||[[MailTo(emlemmon AT ucdavis DOT edu)]]||<br> + ||Brian O'Meara||NESCent||Comparative Methods &amp; Species Delimitation||[[MailTo(bcomeara AT nescent DOT org)]]||<br> + ||Tom Near||Yale||Dating Phylogenetic Trees||[[MailTo(thomas DOT near AT yale DOT edu)]]||<br> + ||Bruce Rannala||UC Davis||Bayesian Inference of Phylogenetic Trees||[[MailTo(brannala AT ucdavis DOT edu)]]||<br> + ||Brad Shaffer||UC Davis||Phylogeography &amp; Species Delimitation||[[MailTo(hbshaffer AT ucdavis DOT edu)]]||<br> + ||Phil Spinks (coordinator)||UC Davis||Phylogenetics||[[MailTo(pqspinks AT ucdavis DOT edu)]]||<br> + ||Bob Thomson||UC Davis||Species Delimitation||[[MailTo(rcthomson AT ucdavis DOT edu)]]||<br> + ||Peter Wainwright||UC Davis||Morphological Diversification||[[MailTo(pcwainwright AT ucdavis DOT edu)]]||<br> + ||Justen Whittall||Santa Clara University||Comparative Methods||[[MailTo(jwhittall AT scu DOT edu)]]||<br> + <br> + <br> + <br> + <br> + [[anchor(finished)]]<br> + =Finished=<br> + ==Pre-Bodega Todo List for Students==<br> + *If you get a chance it would be convenient if you can install some of the software that we'll be using ahead of time. We've compiled a ["Software" list here]. You can wait to do this once you get here, but doing it ahead of time will save time and won't bog down the internet connection at the lab.<br> + *["Getting to Storer Hall" Get yourself to Storer Hall]<br> + *["Reserve Rules"] (they make us distribute these, please read them)<br> + <br> + ==For Sunday==<br> + Download this: [http://www.brianomeara.info/PaupStuff.zip PaupStuff.zip]<br> + Garli dataset: [[File(murphy32.nex)]]<br> + Garli manual: [http://www.phylo.org/pdf_docs/GARLIv0.95manual.pdf manual]<br> + PhyloMapper: [[File(PhyloMapper1b1.zip)]]<br> + <br> + ==For Monday==<br> + '''NOTE: If (and only if) you have an Intel Mac running OS 10.4 or 10.5, please grab a JIST disk at the back of the room, copy its contents to your computer, and return the disk (much faster than downloading)'''<br> + [http://www.brianomeara.info/brownie.zip Brownie] (Intel Macs OS 10.4 or higher) [12.4 MB]<br> + [[File(JistData.zip)]] (Data for the species delimitation exercise)<br> + [[File(marm.in)]] (Data for the structurama exercise)<br> + [[File(Structurama.pdf)]] (handout for the structurama exercise)<br> + <br> + ==For Tuesday==<br> + [[File(Aquilegia.nex)]] (Mesquite Input file for Afternoon Exercises)<br> + [[File(IndependentContrastsExercises.pdf)]] (Tutorial for Afternoon Exercises)<br> + <br> + ==For Wednesday (do this ahead of time, as it DOES require downloads)==<br> + '''New''' Get R file to edit ([[File(randomPoints.R)]]) and the completed one ([[File(randomPointsAnswers.R)]]). You can read more about what we're simulating in [[File(Price1997.pdf)]]<br> + <br> + Get [[File(BrownieHandout.pdf)]], [[File(Results2.xls)]], and [[File(Myrm.nex)]].<br> + Install R (R-2.6.2-win32.exe on a PC, open R2.6.2.dmg on a Mac and run the installer)<br> + Once R is open, install the necessary packages. We want to install '''ape, geiger, ouch''', and '''ade4'''. You can do this by typing '''install.packages()''' and selecting the packages to install. Note that the list is alphabetical, but capital letters are first ('Z' comes before 'a'), so scroll down to get the packages we want.<br> + <br> + BayesTraits Demonstration (Minimum Model of Pollination Syndromes in Columbines by Justen Whittall)<br> + [[File(Bayes Multistate Treefile.txt)]] (Treefile)<br> + [[File(Bayes Multistate Datafile.txt)]] (Datafile)<br> + <br> + <br> + ==For Thursday==<br> + Due to a bug in the most recent version of BEAST, you'll need to get a new version of the tutorial from the thumb drive that is going around the room. Please do this before the beginning of the second morning session.</span> </td> </tr> </table> </div> 2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-17 10:16:58BobThomsonUpload of image <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=2008_class_photo.jpg">2008_class_photo.jpg</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-16 21:42:25Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Bayes%20Multistate%20Datafile.txt">Bayes Multistate Datafile.txt</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-16 21:22:03Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Whittall%20ppt.pdf">Whittall ppt.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-16 14:40:27Upload of image <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Bodega_lunch.jpg">Bodega_lunch.jpg</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-16 14:40:17Upload of image <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Bodega_hike.jpg">Bodega_hike.jpg</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-16 14:40:05Upload of image <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Bodega_work.jpg">Bodega_work.jpg</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 18:16:12Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Price1997.pdf">Price1997.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 18:14:38Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=randomPointsAnswers.R">randomPointsAnswers.R</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 18:13:45Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=randomPoints.R">randomPoints.R</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 16:05:04Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=OMearaBrownieLecture.pdf">OMearaBrownieLecture.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 11:14:23Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Bayes%20Multistate%20Treefile.txt">Bayes Multistate Treefile.txt</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 08:40:24Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Results2.xls">Results2.xls</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 00:20:50Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Myrm.nex">Myrm.nex</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 00:20:12Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Results.xls">Results.xls</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-12 00:19:23Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=BrownieHandout.pdf">BrownieHandout.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-11 15:41:02glorUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Character_Correlation.pdf">Character_Correlation.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-11 14:21:38Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=OMearaSpeciesDelimLecture.pdf">OMearaSpeciesDelimLecture.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-11 08:44:44Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=IndependentContrastsExercises.pdf">IndependentContrastsExercises.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-11 08:42:23Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Aquilegia.nex">Aquilegia.nex</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-10 13:53:04glorUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Character_Evolution_Data.zip">Character_Evolution_Data.zip</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-10 13:52:43glorUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Character_EvolutionII.pdf">Character_EvolutionII.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-10 13:52:09glorUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Character_EvolutionI.pdf">Character_EvolutionI.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-10 09:11:01BobThomsonUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=Structurama.pdf">Structurama.pdf</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-10 09:08:04BobThomsonUpload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=marm.in">marm.in</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-09 22:37:12Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=JistData.zip">JistData.zip</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-09 15:12:22Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=PhyloMapper1b1.zip">PhyloMapper1b1.zip</a>.2008 Workshophttp://bodegaphylo.wikispot.org/2008_Workshop2008-03-09 11:04:10Upload of file <a href="http://bodegaphylo.wikispot.org/2008_Workshop?action=Files&do=view&target=murphy32.nex">murphy32.nex</a>.