Recent Changes for "Front Page" - Bodega Phylogenetics Wiki

Front Page

BobThomson — 2009-06-28 19:41:11

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- ===Welcome to the Bodega Applied Phylogenetics Wiki!===	+ ===Welcome to the Bodega Applied Phylogenetics Wiki===

Front Page

2009-06-11 08:26:49

(quick edit)

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- ===2029 Bodega Applied Phylogenetics Workshop, March 7-14===	+ ===2009 Bodega Applied Phylogenetics Workshop, March 7-14===

Front Page

2009-06-11 08:26:41

(quick edit)

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Front Page

BobThomson — 2009-04-10 04:37:19

Revert to version 240 (reverting to original).

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Front Page

2009-04-10 04:37:05

Revert to version 240 (reverting to original).

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- test	+ ===Welcome to the Bodega Applied Phylogenetics Wiki!=== + This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from estimating phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid). + + You can find tutorials sorted by subject on the ["Topics"] page. ["Contacts" Contact us] with any questions. + ----- + + ===2009 Bodega Applied Phylogenetics Workshop, March 7-14=== + Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. + + We've archived the 2008 course webpage ["2008 Workshop" here]. + [[Image(sunrise_over_dorms.jpg, 220, thumbnail, "Sunrise over the dorms.")]] + [[Image(Point_Reyes_Field_Trip.JPG, 220,thumbnail, "Field Trip to Point Reyes")]] + [[Image(Bodega_work.jpg,220, thumbnail, "Students working on an exercise")]] + + + ===Sponsors=== + [[Image(Bodega_Lab_icon.gif, 150, thumbnail, noborder, "[http://www-bml.ucdavis.edu Bodega Lab]")]] + [[Image(cpb_icon.jpg, 150, thumbnail, noborder, "[http://cpb.ucdavis.edu/ CPB]")]] + [[Image(Rochester_logo.jpg, 150, thumbnail, noborder, "[http://www.rochester.edu/College/BIO/index.php University of Rochester]")]] + [[Image(nescent.png,150, thumbnail, noborder, "[http://www.nescent.org/index.php NESCent]")]]

Front Page

2009-04-10 04:09:50

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- ===Welcome to the Bodega Applied Phylogenetics Wiki!=== - This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from estimating phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid). - - You can find tutorials sorted by subject on the ["Topics"] page. ["Contacts" Contact us] with any questions. - ----- - - ===2009 Bodega Applied Phylogenetics Workshop, March 7-14=== - Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. - - We've archived the 2008 course webpage ["2008 Workshop" here]. - [[Image(sunrise_over_dorms.jpg, 220, thumbnail, "Sunrise over the dorms.")]] - [[Image(Point_Reyes_Field_Trip.JPG, 220,thumbnail, "Field Trip to Point Reyes")]] - [[Image(Bodega_work.jpg,220, thumbnail, "Students working on an exercise")]] - - - ===Sponsors=== - [[Image(Bodega_Lab_icon.gif, 150, thumbnail, noborder, "[http://www-bml.ucdavis.edu Bodega Lab]")]] - [[Image(cpb_icon.jpg, 150, thumbnail, noborder, "[http://cpb.ucdavis.edu/ CPB]")]] - [[Image(Rochester_logo.jpg, 150, thumbnail, noborder, "[http://www.rochester.edu/College/BIO/index.php University of Rochester]")]] - [[Image(nescent.png,150, thumbnail, noborder, "[http://www.nescent.org/index.php NESCent]")]]	+ test

Front Page

GregPauly — 2009-03-24 18:00:19

(quick edit)

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from estimating phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from estimating phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).

Front Page

glor — 2009-03-24 09:27:38

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	+ -----

Front Page

2009-03-20 00:02:42

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from estimating phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).

Front Page

glor — 2009-03-17 09:18:31

Upload of image sunrise_over_dorms.jpg.

Front Page

glor — 2009-03-17 09:18:31

Image sunrise_over_dorms.jpg deleted.

Front Page

glor — 2009-03-17 09:17:00

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- [[Image(2009_Bodega_Bay_Photo_Gallery/CN1.jpg, 220, thumbnail, "Sunrise over the dorms.")]] - [[Image(BB_09_5.JPG, 220,thumbnail, "Lunch on the lab's patio")]]	+ [[Image(sunrise_over_dorms.jpg, 220, thumbnail, "Sunrise over the dorms.")]] + [[Image(Point_Reyes_Field_Trip.JPG, 220,thumbnail, "Field Trip to Point Reyes")]]

Front Page

glor — 2009-03-17 09:16:11

Upload of image Point_Reyes_Field_Trip.JPG.

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glor — 2009-03-17 09:15:13

Upload of image sunrise_over_dorms.jpg.

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glor — 2009-03-17 09:11:31

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- [[Image(2008_class_photo.jpg, 220, thumbnail, "2008 Class Photo")]]	+ [[Image(2009_Bodega_Bay_Photo_Gallery/CN1.jpg, 220, thumbnail, "Sunrise over the dorms.")]] + [[Image(BB_09_5.JPG, 220,thumbnail, "Lunch on the lab's patio")]]
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- [[Image(Bodega_lunch.jpg, 220,thumbnail, "Lunch on the lab's patio")]]	+

Front Page

glor — 2009-03-15 17:13:45

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- ''During the week of March 7-March 14, 2009 this page will be undergoing major updates. Check back daily for the latest.'' -

Front Page

glor — 2009-03-13 13:18:34

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- ===2009 Bodega Applied Phylogenetics Workshop=== - Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009 Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) is far too slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application.	+ ===2009 Bodega Applied Phylogenetics Workshop, March 7-14=== + Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement.

Front Page

glor — 2009-03-13 13:17:18

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and [Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the [Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with [Community Phylogenetics Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and ["Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the ["Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with ["Community Phylogenetics" Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).

Front Page

glor — 2009-03-13 13:16:44

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- ''During the week of March 7-March 14, 2009 this page will be undergoing major updates. Check back daily for the latest.'''	+ ''During the week of March 7-March 14, 2009 this page will be undergoing major updates. Check back daily for the latest.''

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glor — 2009-03-13 13:16:33

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- '''If you are a student in the 2009 Bodega Workshop, go to the ["2009 Workshop" 2009 workshop webpage].''' - '''During the week of March 7-March 14, 2009 this page will be undergoing a major update. Check back daily for updates.'''	+ ''During the week of March 7-March 14, 2009 this page will be undergoing major updates. Check back daily for the latest.'''
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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees using programs like MrBayes and Garli to testing character correlation with programs like BayesTraits, R, and Mesquite. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees with programs like ["MrBayes Tutorial" MrBayes] and [Maximum Likelihood (GARLI 0.96)" Garli] to testing patterns of character evolution with the packages available in the [Phylogenetics and Comparative Methods in R" R] framework to investigating patterns of community evolution with [Community Phylogenetics Phylocom]. We hope you find this Wiki useful and easy to use. If you're having a trouble understanding any of the material you find here, let us know. Better still, you can make some changes of your own. If you'd like to become a contributor, there is a ["Wiki Quickstart" short guide] to get you started. You don't need our permission to become a contributor or to make changes to our pages (although we will be keeping tabs on things to make sure people don't do anything stupid).
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- You can find the tutorials sorted by subject on the ["Topics"] page. ["Contacts" Contact us] with any questions.	+ You can find tutorials sorted by subject on the ["Topics"] page. ["Contacts" Contact us] with any questions.

Front Page

BobThomson — 2009-03-12 10:29:10

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- Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009 Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) if far to slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application.	+ Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009 Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) is far too slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application.

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glor — 2009-03-09 20:07:45

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- '''During the week of March 7-March 14 this page will be undergoing a major update. Check back daily for updates.'''	+ '''During the week of March 7-March 14, 2009 this page will be undergoing a major update. Check back daily for updates.'''

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glor — 2009-03-09 20:07:34

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- '''If you are a student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage].'''	+ '''If you are a student in the 2009 Bodega Workshop, go to the ["2009 Workshop" 2009 workshop webpage].''' + '''During the week of March 7-March 14 this page will be undergoing a major update. Check back daily for updates.'''
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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community can use. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're in the process of 'wikifying' a series of existing tutorials now. We're counting on the rest of the community to help us keep these tutorials current, and perhaps even add some new ones. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We're building a set of step-by-step tutorials on everything from reconstructing phylogenetic trees using programs like MrBayes and Garli to testing character correlation with programs like BayesTraits, R, and Mesquite. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.

Front Page

glor — 2009-03-08 09:11:31

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- You can find the tutorials sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.	+ You can find the tutorials sorted by subject on the ["Topics"] page. ["Contacts" Contact us] with any questions.

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glor — 2009-03-08 09:07:18

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- ====Sponsors====	+ ===Sponsors===

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glor — 2009-03-08 09:05:10

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- =Welcome to the Bodega Applied Phylogenetics Wiki!=	+ ===Welcome to the Bodega Applied Phylogenetics Wiki!===
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- =2009 Bodega Applied Phylogenetics Workshop=	+ ===2009 Bodega Applied Phylogenetics Workshop===
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- ==["2009 Workshop" 2009 workshop webpage]==	+ ====["2009 Workshop" 2009 workshop webpage]====
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- =Sponsors=	+ ====Sponsors====

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2009-03-08 08:51:24

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- '''If you area student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage].'''	+ '''If you are a student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage].'''

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2009-03-08 07:34:57

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- If you area student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage].	+ '''If you area student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage].'''

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2009-03-08 07:34:25

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	+ If you area student in the 2009 Bodega Workshop, please go to the ["2009 Workshop" 2009 workshop webpage]. + +

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BobThomson — 2009-03-01 20:59:48

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- Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009_Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) if far to slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application.	+ Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009 Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) if far to slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application.

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glor — 2009-03-01 13:22:35

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- Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement.	+ Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement. If you will be participating in the 2009 course, it is important that you go to the ["2009_Workshop"] page and download and install all of the applications listed under the course materials. You must do this before arriving at Bodega Bay, our internet connection (if available) if far to slow to permit the required downloads. Be sure to do the preliminary R "Getting Started" exercises if you hope to follow along with the portions of the course that require use of this application. +

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BobThomson — 2009-02-18 10:39:15

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- - [[Include(Topics, "Topics")]]

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BobThomson — 2009-02-18 10:38:30

cleaning up

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- - - =2009 Course Materials= - ["Go here for 2009 Course Materials"]

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BobThomson — 2009-02-18 10:21:55

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- We've archived the 2008 course webpage ["2008 Workshop" here].	+ ==["2009 Workshop" 2009 workshop webpage]== +
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	+ We've archived the 2008 course webpage ["2008 Workshop" here].

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BobThomson — 2009-02-18 10:17:19

minor edits

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- Prospective students for the 2009 workshop have now being accepted. Check back next winter (December 2009) for next year's announcement.	+ Prospective students for the 2009 workshop have now been accepted. Check back next winter (December 2009) for next year's announcement.

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PhillipSpinks — 2009-02-11 12:12:14

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	+ We've archived the 2008 course webpage ["2008 Workshop" here].
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- We've archived the 2008 course webpage ["2008 Workshop" here].	+ =2009 Course Materials= + ["Go here for 2009 Course Materials"]

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PhillipSpinks — 2009-01-16 13:11:56

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- . We've archived the 2008 course webpage ["2008 Workshop" here].	+ We've archived the 2008 course webpage ["2008 Workshop" here].

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PhillipSpinks — 2009-01-16 13:11:33

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- Applications for the 2009 workshop are now being accepted. The course announcement and application information is posted ["2009 Course Announcement" here]. We've archived the 2008 course webpage ["2008 Workshop" here].	+ Prospective students for the 2009 workshop have now being accepted. Check back next winter (December 2009) for next year's announcement. + + . We've archived the 2008 course webpage ["2008 Workshop" here].

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BobThomson — 2008-12-02 09:41:20

posting 2009 announcement

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- Interested in attending our next workshop in person? The ["2008 Workshop" 2008 workshop] is over, but the ["2008 Advertisement" course announcement] might answer some of your basic questions. An advertisement for the 2009 workshop will go out next fall.	+ =2009 Bodega Applied Phylogenetics Workshop= + Applications for the 2009 workshop are now being accepted. The course announcement and application information is posted ["2009 Course Announcement" here]. We've archived the 2008 course webpage ["2008 Workshop" here].
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- - =2008 Bodega Applied Phylogenetics Workshop= - - The ninth year of the Bodega workshop wrapped up on March 15th, 2008. This year we had 36 students representing six countries. We covered more material and worked harder this year than ever before. Everyone learned a ton (instructors included) and a good time was had by all. We've archived the 2008 course webpage ["2008 Workshop" here].

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BobThomson — 2008-06-22 14:14:34

cleaning up

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're in the process of 'wikifying' a series of existing tutorials now. We're counting on the rest of the community to help us keep these tutorials current, and perhaps even add some new ones. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community can use. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're in the process of 'wikifying' a series of existing tutorials now. We're counting on the rest of the community to help us keep these tutorials current, and perhaps even add some new ones. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.
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- You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.	+ You can find the tutorials sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.

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glor — 2008-05-06 15:41:22

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're hoping the rest of you can help us keep these tutorial current, and perhaps even add some new ones of your own. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're in the process of 'wikifying' a series of existing tutorials now. We're counting on the rest of the community to help us keep these tutorials current, and perhaps even add some new ones. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.
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- We're in the process of 'wikifying' a series of existing tutorials. You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.	+ You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.

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glor — 2008-05-05 21:29:02

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're hoping the rest of you can help us keep these tutorial current, and perhaps even add some new ones of your own. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're hoping the rest of you can help us keep these tutorial current, and perhaps even add some new ones of your own. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.
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- We are in the process of 'wikifying' a series of tutorials. You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.	+ We're in the process of 'wikifying' a series of existing tutorials. You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.
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glor — 2008-05-05 21:27:42

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into a general resource for members of the phylogenetics community. We've elected the wiki format because it's remarkably easy to use; if you'd like to become a contributor, we've 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.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will grow into an important instructional resource the entire phylogenetics community. We've elected the Wiki format because we're going to need your help! Our team will start things off with a series of basic tutorials on everything from conducting a modern phylogenetic analysis in MrBayes to testing character correlation in a phylogenetic context with programs like BayesTraits, R, and Mesquite. We're hoping the rest of you can help us keep these tutorial current, and perhaps even add some new ones of your own. The Wiki is remarkably easy to use and offers instant gratification. If you'd like to become a contributor, here's a ["Wiki Quickstart" short guide] to get you started.
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- Interested in attending the workshop? The ["2008 Workshop" 2008 workshop] just finished, though the ["2008 Advertisement" course announcement] contains general information about the course that might answer some of your questions about next year's course. A new advertisement will go out next fall for the spring 2009 workshop.	+ We are in the process of 'wikifying' a series of tutorials. You can check find theme sorted by subject on the ["Topics"] page. Want to request a tutorial? Post it on the ["Wanted"] page. ["Contacts" Contact us] with any questions.
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- We are in the process of 'wikifying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Topics"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].	+ Interested in attending our next workshop in person? The ["2008 Workshop" 2008 workshop] is over, but the ["2008 Advertisement" course announcement] might answer some of your basic questions. An advertisement for the 2009 workshop will go out next fall. + +

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glor — 2008-05-02 09:22:31

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- [[Image(Bodega_Lab_icon.gif, 150, thumbnail, noborder)]] - [[Image(cpb_icon.jpg, 150, thumbnail, noborder)]] - [[Image(Rochester_logo.jpg, 150, thumbnail, noborder)]] - [[Image(nescent.png,150, thumbnail, noborder)]]	+ [[Image(Bodega_Lab_icon.gif, 150, thumbnail, noborder, "[http://www-bml.ucdavis.edu Bodega Lab]")]] + [[Image(cpb_icon.jpg, 150, thumbnail, noborder, "[http://cpb.ucdavis.edu/ CPB]")]] + [[Image(Rochester_logo.jpg, 150, thumbnail, noborder, "[http://www.rochester.edu/College/BIO/index.php University of Rochester]")]] + [[Image(nescent.png,150, thumbnail, noborder, "[http://www.nescent.org/index.php NESCent]")]]

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glor — 2008-04-28 19:08:44

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- This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. Although initially intended as a tool for instructors and students to share files, datasets, links, and other information, we hope it will now grow into a more general resource for members of the phylogenetics community. We've elected the wiki format because it is remarkably easy to use; if you'd like to become a contributor, we've 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.	+ This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. We hope it will now grow into a general resource for members of the phylogenetics community. We've elected the wiki format because it's remarkably easy to use; if you'd like to become a contributor, we've 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.
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- Interested in attending the workshop? The ["2008 Workshop" 2008 workshop] just finished, though the ["2008 Advertisement" course announcement] contains general information about the course that might answer some of your questions. A new advertisement will go out next fall for the spring 2009 workshop.	+ Interested in attending the workshop? The ["2008 Workshop" 2008 workshop] just finished, though the ["2008 Advertisement" course announcement] contains general information about the course that might answer some of your questions about next year's course. A new advertisement will go out next fall for the spring 2009 workshop.

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glor — 2008-03-20 06:17:36

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- The ninth year of the Bodega workshop just finished up. We covered more material and worked harder this year than ever before. Everyone learned a ton (instructors included) and a good time was had by all. We've archived the 2008 course webpage ["2008 Workshop" here].	+ The ninth year of the Bodega workshop wrapped up on March 15th, 2008. This year we had 36 students representing six countries. We covered more material and worked harder this year than ever before. Everyone learned a ton (instructors included) and a good time was had by all. We've archived the 2008 course webpage ["2008 Workshop" here].

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glor — 2008-03-19 15:23:02

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- [[Image(Bodega_Lab_icon.gif, 300, thumbnail, noborder)]] - [[Image(cpb_icon.jpg, 300, thumbnail, noborder)]] - [[Image(Rochester_logo.jpg, 300, thumbnail, noborder)]] - [[Image(nescent.png,300, thumbnail, noborder)]]	+ [[Image(Bodega_Lab_icon.gif, 150, thumbnail, noborder)]] + [[Image(cpb_icon.jpg, 150, thumbnail, noborder)]] + [[Image(Rochester_logo.jpg, 150, thumbnail, noborder)]] + [[Image(nescent.png,150, thumbnail, noborder)]]

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BobThomson — 2008-03-19 14:37:22

nescent gave us money too

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BobThomson — 2008-03-19 14:36:31

Upload of image nescent.png.

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glor — 2008-03-19 14:01:52

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glor — 2008-03-19 14:01:37

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glor — 2008-03-19 14:01:30

Upload of image cpb_icon.jpg.

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glor — 2008-03-19 14:01:16

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glor — 2008-03-19 13:56:48

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glor — 2008-03-19 13:56:20

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glor — 2008-03-19 13:52:54

Upload of image Rochester_logo.jpg.

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glor — 2008-03-19 13:50:17

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glor — 2008-03-19 13:49:38

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glor — 2008-03-19 13:47:57

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glor — 2008-03-19 13:47:35

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glor — 2008-03-19 13:47:24

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glor — 2008-03-19 13:47:11

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glor — 2008-03-19 13:46:51

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glor — 2008-03-19 13:46:33

Upload of image Bodega_Lab_icon.gif.

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glor — 2008-03-19 13:44:57

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BobThomson — 2008-03-19 13:14:46

dropping 'Tutorials' and going with 'Topics'

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BobThomson — 2008-03-19 12:42:14

(quick edit)

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- We are in the process of 'wikifying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].	+ We are in the process of 'wikifying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Topics"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].

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glor — 2008-03-19 11:52:48

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- Welcome to the Bodega Applied Phylogenetics Wiki! This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. Although initially intended as a tool for instructors and students to share files, datasets, links, and other information, we hope it will now grow into a more general resource for members of the phylogenetics community. We've elected the wiki format because it is remarkably easy to use; if you'd like to become a contributor, we've 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.	+ =Welcome to the Bodega Applied Phylogenetics Wiki!= + This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. Although initially intended as a tool for instructors and students to share files, datasets, links, and other information, we hope it will now grow into a more general resource for members of the phylogenetics community. We've elected the wiki format because it is remarkably easy to use; if you'd like to become a contributor, we've 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.

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glor — 2008-03-19 11:26:31

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- Welcome to the Bodega 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 wiki was initially created as tool for instructors and students to share files, datasets, links, and other information, and is now growing into a more general resource for the course as well as the phylogenetics community in general. 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.	+ Welcome to the Bodega Applied Phylogenetics Wiki! This wiki is an extension of the week-long workshop in applied phylogenetics held each Spring at the Bodega Bay Marine Lab. Although initially intended as a tool for instructors and students to share files, datasets, links, and other information, we hope it will now grow into a more general resource for members of the phylogenetics community. We've elected the wiki format because it is remarkably easy to use; if you'd like to become a contributor, we've 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.

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glor — 2008-03-19 11:18:21

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- [[Image(Bodega_work.jpg,220 thumbnail, "Students working on an exercise")]]	+ [[Image(Bodega_work.jpg,220, thumbnail, "Students working on an exercise")]]

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glor — 2008-03-19 11:17:22

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glor — 2008-03-19 11:16:07

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2008-03-19 11:06:44

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- [[Image(2008_class_photo.jpg, 500, right, thumbnail, "2008 Class Photo")]] - [[Image(Bodega_work.jpg,250, thumbnail, "Students working on an exercise")]] - [[Image(Bodega_lunch.jpg, 250,thumbnail, "Lunch on the lab's patio")]]	+ [[Image(2008_class_photo.jpg, 220, thumbnail, "2008 Class Photo")]] + [[Image(Bodega_work.jpg,220 thumbnail, "Students working on an exercise")]] + [[Image(Bodega_lunch.jpg, 220,thumbnail, "Lunch on the lab's patio")]]

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BobThomson — 2008-03-19 09:25:42

(quick edit)

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- We are in the process of 'wiki-fying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].	+ We are in the process of 'wikifying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].

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BobThomson — 2008-03-19 09:24:59

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BobThomson — 2008-03-19 09:23:55

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BobThomson — 2008-03-19 09:06:12

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- We are in the process of 'wiki-fying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page.	+ We are in the process of 'wiki-fying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. If you have questions ["Contacts" contact us].

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BobThomson — 2008-03-19 09:03:28

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- 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.	+ Welcome to the Bodega 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 wiki was initially created as tool for instructors and students to share files, datasets, links, and other information, and is now growing into a more general resource for the course as well as the phylogenetics community in general. 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. + + Interested in attending the workshop? The ["2008 Workshop" 2008 workshop] just finished, though the ["2008 Advertisement" course announcement] contains general information about the course that might answer some of your questions. A new advertisement will go out next fall for the spring 2009 workshop. + + We are in the process of 'wiki-fying' the tutorials from this year. If you're trying to figure out how to do something, check them out on the ["Tutorials"] page, we may have covered it. Want to request a tutorial? Post it on the ["Wanted"] page. + + =2008 Bodega Applied Phylogenetics Workshop= + + The ninth year of the Bodega workshop just finished up. We covered more material and worked harder this year than ever before. Everyone learned a ton (instructors included) and a good time was had by all. We've archived the 2008 course webpage ["2008 Workshop" here]. + + [[Image(2008_class_photo.jpg, 500, right, thumbnail, "2008 Class Photo")]] + [[Image(Bodega_work.jpg,250, thumbnail, "Students working on an exercise")]] + [[Image(Bodega_lunch.jpg, 250,thumbnail, "Lunch on the lab's patio")]]

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BobThomson — 2008-03-19 08:54:46

Upload of image Bodega_work.jpg.

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BobThomson — 2008-03-19 08:54:46

Image Bodega_work.jpg deleted.

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BobThomson — 2008-03-19 08:37:23

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BobThomson — 2008-03-19 08:33:16

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BobThomson — 2008-03-19 08:31:19

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- #redirect 2008 Workshop	+ 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.

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BobThomson — 2008-03-19 08:28:14

Renamed to "2008 Workshop"

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- 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. - - - =2008 Workshop= - [[Image(2008_class_photo.jpg, 700, thumbnail, "2008 Workshop Participants")]] - - [[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")]] - - - [[anchor(2008 Schedule)]] - =Schedule= - \|\|<tableborder="1" tablewidth="70%" rowbgcolor="#FFFFE0" align="center">\|\|'''Morning'''\|\|'''Afternoon'''\|\|'''Evening'''\|\| - \|\|'''Saturday'''\|\|<#E0E0FF>\|\|Arrivals\|\|Setup ["Student Projects"]\|\| - \|\|'''Sunday'''\|\|["Phylogenetics Medley"] '''([http://bodegaphylo.wikispot.org/Phylogenetics_Medley?action=Files&do=view&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&do=view&target=PaupLecture.pdf lecture pdf])'''\|\|["Bayesian Phylogenetics (Rannala)"]\|\|["Phylogeography (Lemmon & Lemmon)"]\|\| - \|\|'''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)"]\|\| - \|\|'''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)"]\|\| - \|\|'''Wednesday'''\|\|["Morphological Diversification (Wainwright & O'Meara)"] ('''[[File(OMearaBrownieLecture.pdf)]]''')\|\|FIELD TRIPS\|\|["NESCent overview (O'Meara)"]/ ["R Tutorial (Glor & O'Meara)"]\|\| - \|\|'''Thursday'''\|\|["Divergence Times & BEAST tutorial (Moore)"]\|\|["Diversification Rates (Moore)"]\|\|Work on Projects (also a ["Bay Area Biosystematists meeting"])\|\| - \|\|'''Friday'''\|\|Finish up projects & Begin Presentations\|\|More Student Presentations\|\|Free\|\| - \|\|'''Saturday'''\|\|Pack up and go home\|\|<#E0E0FF> \|\|<#E0E0FF> \|\| - - - =Instructors= - \|\| \|\|'''Institution'''\|\|'''Topic'''\|\|'''Email'''\|\| - \|\|Kevin de Queiroz\|\|Smithsonian Institution\|\|Species & Rank Free Taxonomy\|\|[[MailTo(dequeirozk AT si DOT edu)]]\|\| - \|\|Jonathan Eisen\|\|UC Davis\|\|Phylogenomics\|\|[[MailTo(jaeisen AT ucdavis DOT edu)]]\|\| - \|\|Rich Glor\|\|University of Rochester\|\|Comparative Methods\|\|[[MailTo(rglor AT mail DOT rochester DOT edu)]]\|\| - \|\|Alan Lemmon\|\|UC Davis\|\|Phylogeographic Methods\|\|[[MailTo(arlemmon AT ucdavis DOT edu)]]\|\| - \|\|Brent Mishler\|\|UC Berkeley\|\|Rank Free Taxonomy\|\|[[MailTo(BMishler AT calmail DOT berkeley DOT edu)]]\|\| - \|\|Brian Moore\|\|UC Berkeley\|\|Species Diversification\|\|[[MailTo(brian DOT moore AT yale DOT edu)]]\|\| - \|\|Emily Moriarty Lemmon\|\|UC Davis\|\|Phylogeographic Methods\|\|[[MailTo(emlemmon AT ucdavis DOT edu)]]\|\| - \|\|Brian O'Meara\|\|NESCent\|\|Comparative Methods & Species Delimitation\|\|[[MailTo(bcomeara AT nescent DOT org)]]\|\| - \|\|Tom Near\|\|Yale\|\|Dating Phylogenetic Trees\|\|[[MailTo(thomas DOT near AT yale DOT edu)]]\|\| - \|\|Bruce Rannala\|\|UC Davis\|\|Bayesian Inference of Phylogenetic Trees\|\|[[MailTo(brannala AT ucdavis DOT edu)]]\|\| - \|\|Brad Shaffer\|\|UC Davis\|\|Phylogeography & Species Delimitation\|\|[[MailTo(hbshaffer AT ucdavis DOT edu)]]\|\| - \|\|Phil Spinks (coordinator)\|\|UC Davis\|\|Phylogenetics\|\|[[MailTo(pqspinks AT ucdavis DOT edu)]]\|\| - \|\|Bob Thomson\|\|UC Davis\|\|Species Delimitation\|\|[[MailTo(rcthomson AT ucdavis DOT edu)]]\|\| - \|\|Peter Wainwright\|\|UC Davis\|\|Morphological Diversification\|\|[[MailTo(pcwainwright AT ucdavis DOT edu)]]\|\| - \|\|Justen Whittall\|\|Santa Clara University\|\|Comparative Methods\|\|[[MailTo(jwhittall AT scu DOT edu)]]\|\| - - - - - [[anchor(finished)]] - =Finished= - ==Pre-Bodega Todo List for Students== - 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. - ["Getting to Storer Hall" Get yourself to Storer Hall] - *["Reserve Rules"] (they make us distribute these, please read them) - - ==For Sunday== - Download this: [http://www.brianomeara.info/PaupStuff.zip PaupStuff.zip] - Garli dataset: [[File(murphy32.nex)]] - Garli manual: [http://www.phylo.org/pdf_docs/GARLIv0.95manual.pdf manual] - PhyloMapper: [[File(PhyloMapper1b1.zip)]] - - ==For Monday== - '''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)''' - [http://www.brianomeara.info/brownie.zip Brownie] (Intel Macs OS 10.4 or higher) [12.4 MB] - [[File(JistData.zip)]] (Data for the species delimitation exercise) - [[File(marm.in)]] (Data for the structurama exercise) - [[File(Structurama.pdf)]] (handout for the structurama exercise) - - ==For Tuesday== - [[File(Aquilegia.nex)]] (Mesquite Input file for Afternoon Exercises) - [[File(IndependentContrastsExercises.pdf)]] (Tutorial for Afternoon Exercises) - - ==For Wednesday (do this ahead of time, as it DOES require downloads)== - '''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)]] - - Get [[File(BrownieHandout.pdf)]], [[File(Results2.xls)]], and [[File(Myrm.nex)]]. - Install R (R-2.6.2-win32.exe on a PC, open R2.6.2.dmg on a Mac and run the installer) - 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. - - BayesTraits Demonstration (Minimum Model of Pollination Syndromes in Columbines by Justen Whittall) - [[File(Bayes Multistate Treefile.txt)]] (Treefile) - [[File(Bayes Multistate Datafile.txt)]] (Datafile) - - - ==For Thursday== - 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.	+ #redirect 2008 Workshop

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- '''New''': Just a note that might help with running PAUP, etc. -- there's a somewhat dated guide to using PAUP, creating batch files, etc. at [http://www.brianomeara.info/phylogenetics.html Phylogenetic Analysis]

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BobThomson — 2008-03-17 13:00:18

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- *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. We also have ["Papers" papers] to read.	+ *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.

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BobThomson — 2008-03-17 12:58:44

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	+ \|\| \|\|'''Institution'''\|\|'''Topic'''\|\|'''Email'''\|\|

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BobThomson — 2008-03-17 12:30:54

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BobThomson — 2008-03-17 12:21:52

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BobThomson — 2008-03-17 10:41:35

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- Welcome to the Applied Phylogenetics Wiki! This wiki has grown from a week-long workshop in applied phylogenetic 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 at the [#QuickStart bottom of this page]. Virtually everything is edit-able and there is no need to log in (although this may soon change), so feel free to add or change content.	+ 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.
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- [[anchor(QuickStart)]] - A brief guide to things you might want to do. - - '''Editing Existing Pages''' - Go to the page you want to edit and click on the 'edit' link at the top of the page. (for really simple edits, you can just double click the block of text you want to change) - '''Common editing tasks:''' - ''editing text'' - Just type and delete text in the editor window then hit the 'save changes' button. There are some simple formatting directions below the editor (e.g. '''Bold''', ''italics'', etc.) - ''creating links'' - to link to another page IN the wiki just type {{{["page name"]}}} in an editor window, to link OUT of the wiki type {{{[http://www.webpage.com]}}} (note that quotes aren't used for linking out). - ''uploading files'' - Click the 'upload files' button at the bottom of the editor window. Choose a file and give it a name in the 'Save as' box then hit the 'upload' button. Link to the file on your page by typing {{{[[File(filename)]]}}} in the editor window. - ''displaying images'' - to display an image, upload it exactly the same way as with a file, then link to it by typing {{{[[Image(filename)]]}}} . - '''Adding New Pages''' - Create a link from an existing page to the (currently non-existent) page you want to make by typing {{{["New Page's Title"]}}}, click on the link and hit 'Create this page'. Your new page will open in an editor window. - '''Deleting Pages''' - It's easiest just to tell Bob to do this for you. - If you want to play around to get a feel for how things work head over to the ["Wiki Sandbox"]. - More detail on editing can be found [wiki:wikispot:"Help with Editing" here]

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BobThomson — 2008-03-17 09:25:24

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- (Older datasets and downloads have been moved [#finished here]).
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BobThomson — 2008-03-17 09:24:07

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- [[Image(Bodega_work.jpg, thumbnail, "Students working on an exercise")]][[Image(Bodega_lunch.jpg, thumbnail, "Lunch on the lab's patio")]][[Image(Bodega_hike.jpg, thumbnail, "Peter Wainwright's annual beach hike")]]	+ [[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")]]

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BobThomson — 2008-03-17 09:16:58

Upload of image 2008_class_photo.jpg.

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2008-03-17 08:41:41

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- \|\|'''Tuesday'''\|\|["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstruction.pdf 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)"]\|\|	+ \|\|'''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)"]\|\|

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2008-03-17 08:40:23

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2008-03-17 08:40:17

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- \|\|'''Tuesday'''\|\|["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstructions.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)"]\|\|	+ \|\|'''Tuesday'''\|\|["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstruction.pdf 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)"]\|\|

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2008-03-17 08:38:28

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- \|\|'''Tuesday'''\|\|["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstructions.pdf Ancestral_Reconstructions.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)"]\|\|	+ \|\|'''Tuesday'''\|\|["Comparative Methods I (Glor)"] (Lectures: '''[http://www.brianomeara.info/BodegaPresentations/Ancestral_Reconstructions.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)"]\|\|

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BobThomson — 2008-03-17 07:07:03

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- \|\|Bruce Rannala\|\|UC Davis\|\|Bayesian Inference of Phylogenetic Tree\|\|[[MailTo(brannala AT ucdavis DOT edu)]]\|\|	+ \|\|Bruce Rannala\|\|UC Davis\|\|Bayesian Inference of Phylogenetic Trees\|\|[[MailTo(brannala AT ucdavis DOT edu)]]\|\|

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2008-03-16 20:42:50

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- BayesTraits	+ BayesTraits Demonstration (Minimum Model of Pollination Syndromes in Columbines by Justen Whittall)
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	+ [[File(Bayes Multistate Datafile.txt)]] (Datafile)

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2008-03-16 20:42:25

Upload of file Bayes Multistate Datafile.txt.