Recent Changes - Bodega Phylogenetics Wiki

VI. Testing Temporal Patterns of Character Evolution in R

2009-10-13 01:21:42

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- {{{deltaTransform(anolisComparativeTree, 50) -> anolisDelta0}}}	+ {{{deltaTransform(anolisComparativeTree, 50) -> anolisDelta50}}}

MrBayes Tutorial

BobThomson — 2009-10-06 07:13:13

Typo fixed. Thanks.

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- When we read this block into MrBayes, we will get a partitioned model with the first character division being the first position of the codon, the second division being the second position of the codon etc. In addition, we want a separate model for each partition. Thus, all the parameters should be estimated separately for the individual data partitions. Assume further that we want the overall evolutionary rate to be allowed to vary across different partitions. We can obtain this model by using lset and prset with the applyto mechanism, which allows us to apply the settings to specific partition. With the MrBayes block above, we applied an HKY + G model to the 1st and 2nd partitions, and a GTR+G+I model to the 3rd partition, we could also enter these commands through the command line by typing lset applyto=(1,2) nst=2 rates=gamma, and prset applyto=(1,2) pinvarpr=fixed(0). This takes care of partitions 1 and 2, and lset applyto=(3) nst=6 rates=invgamma would set the model for the 3rd partition.	+ When we read this block into MrBayes, we will get a partitioned model with the first character division being the first position of the codon, the second division being the second position of the codon etc. In addition, we want a separate model for each partition. Thus, all the parameters should be estimated separately for the individual data partitions. Assume further that we want the overall evolutionary rate to be allowed to vary across different partitions. We can obtain this model by using lset and prset with the applyto mechanism, which allows us to apply the settings to specific partition. With the MrBayes block above, we applied an HKY + G model to the 1st and 2nd partitions, and a GTR+G+I model to the 3rd partition, we could also enter these commands through the command line by typing lset applyto=(1,2) nst=2 rates=gamma, and prset applyto=(1,2) pinvarpr=fixed(0). This takes care of partitions 1 and 2, and lset applyto=(3) nst=6 rates=gamma would set the model for the 3rd partition.
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- ------ - ''2009-10-06 06:49:15'' [[nbsp]] "lset applyto=(3) nst=6 rates=gamma;" is given in the mrbayes block. "not lset applyto=(3) nst=6 rates=invgamma;" is given in the text --141.213.176.20

MrBayes Tutorial

2009-10-06 05:49:15

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	+ ------ + ''2009-10-06 06:49:15'' [[nbsp]] "lset applyto=(3) nst=6 rates=gamma;" is given in the mrbayes block. "not lset applyto=(3) nst=6 rates=invgamma;" is given in the text --141.213.176.20

Structure

2009-08-22 04:38:57

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	+ ------ + ''2009-08-22 05:38:57'' [[nbsp]] Dear Sir, Please help me to prepare input file for SSR data + SOURABH KUMAR DAS + Research Fellow, + Tocklai Experimental Station, + Tea Research Association, + Jorhat. Assam. India + Sourabhkrdas@gmail.com --124.247.205.200

Users/PeterCowman

BobThomson — 2009-07-31 11:43:19

Renamed from "Peter Cowman" (changing to match naming convention)

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	+ \|\|<bgcolor='#E0E0FF'>'''TITLE'''\|\| + \|\|Rabbitfish (Siganus) Diversification\|\| + \|\|<bgcolor='#E0E0FF'>'''PEOPLE'''\|\| + \|\|Peter Cowman\|\| + + + Email: peter.cowman@jcu.edu.au + + Project Files + [[File(Siganus.nex)]] + + Publications: + Cowman et al., 2009. Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs. MPE

Peter Cowman

BobThomson — 2009-07-31 11:43:18

Renamed to "Users/PeterCowman"

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- \|\|<bgcolor='#E0E0FF'>'''TITLE'''\|\| - \|\|Rabbitfish (Siganus) Diversification\|\| - \|\|<bgcolor='#E0E0FF'>'''PEOPLE'''\|\| - \|\|Peter Cowman\|\| - - - Email: peter.cowman@jcu.edu.au - - Project Files - [[File(Siganus.nex)]] - - Publications: - Cowman et al., 2009. Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs. MPE	+ #redirect Users/PeterCowman

Users/BobThomson

BobThomson — 2009-07-31 08:19:53

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- \|\|[http://www2.eve.ucdavis.edu/rcthomson]\|\|	+ \|\|[http://www.eve.ucdavis.edu/rcthomson]\|\|

Biogeography (Donoghue & Smith)

2009-07-28 01:17:46

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	+ ------ + ''2009-07-28 02:17:46'' [[nbsp]] I can not undersatand how to operate it still! + Would you like teach me step by step ? + My e-mail :amingkong@gmail.com + Thank you! --59.50.64.70

Advice for Aspiring Phylogeneticists

2009-07-02 12:37:27

noticed a gammar error, and did a slight rewording

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- Consider reading [http://catb.org/esr/faqs/smart-questions.html this] to help understand how developer like to see questions structured. Providing details and output will help you get answers from developers and mailing lists quicker.	+ Consider reading [http://catb.org/esr/faqs/smart-questions.html this] to help understand how developers like to see questions structured. Providing details (like program and error output) will help you get answers from developers and mailing lists quicker.

Advice for Aspiring Phylogeneticists

2009-07-02 12:36:06

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	+ Consider reading [http://catb.org/esr/faqs/smart-questions.html this] to help understand how developer like to see questions structured. Providing details and output will help you get answers from developers and mailing lists quicker. +

Generating Species Trees with BEST

BobThomson — 2009-07-02 08:58:21

(quick edit)

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- {{{prset thetapr=invgamma(3,0.003) GeneMuPr=uniform(0.5,1.5) poissonmean=1 BEST=1;}}}	+ {{{prset thetapr=invgamma(3,0.003) GeneMuPr=uniform(0.5,1.5) poissonmean=5 BEST=1;}}}

Peter Cowman

PeterCowman — 2009-06-29 16:50:59

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- Publications	+ Publications:

Peter Cowman

PeterCowman — 2009-06-29 16:50:29

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- ["http://www.science-direct.com/science?_ob=ArticleURL&_udi=B6WNH-4WBK7BK-1&_user=972264&_coverDate=05%2F21%2F2009&_rdoc=37&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236963%239999%23999999999%2399999%23FLA%23display%23Articles)&_cdi=6963&_sort=d&_docanchor=&view=c&_ct=75&_acct=C000049659&_version=1&_urlVersion=0&_userid=972264&md5=add9d5d5d667deb281cb008416bb6d28"]

Peter Cowman

PeterCowman — 2009-06-29 16:49:44

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	+ + Publications + Cowman et al., 2009. Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs. MPE + ["http://www.science-direct.com/science?_ob=ArticleURL&_udi=B6WNH-4WBK7BK-1&_user=972264&_coverDate=05%2F21%2F2009&_rdoc=37&_fmt=high&_orig=browse&_srch=doc-info(%23toc%236963%239999%23999999999%2399999%23FLA%23display%23Articles)&_cdi=6963&_sort=d&_docanchor=&view=c&_ct=75&_acct=C000049659&_version=1&_urlVersion=0&_userid=972264&md5=add9d5d5d667deb281cb008416bb6d28"]

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===

Structure

BobThomson — 2009-06-23 09:24:09

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- For K=3, ''Structure'' cleanly splits the Southern CA population from San Joaquin, while the Santa Barbara population appears to be drawn from each of these clusters. The northern population remains relatively unchanged. So K=3 is a better fit statistically, and it appears to capture more sturcture in the data than K=2. When we move to K=4, little changes except that the Northern/SB/Monterey cluster splits into two clusters with each individual admixed from both clusters. This occurs because the Northern population consists of largely invariant individuals. Because little variation exists, little change in Hardy-Weinberg equilibrium occurs by splitting the individuals into more and more populations and so the program chooses this as the least costly place to introduce an additional cluster. Clearly this doesn't make biological sense, so in this case I'd say K=3 provides the best fit to the data.	+ For K=3, ''Structure'' cleanly splits the Southern CA population from San Joaquin, while the Santa Barbara population appears to be drawn from each of these clusters. The northern population remains relatively unchanged. So K=3 is a better fit statistically, and it appears to capture more structure in the data than K=2. When we move to K=4, little changes except that the Northern/SB/Monterey cluster splits into two clusters with each individual admixed from both clusters. This occurs because the Northern population consists of largely invariant individuals. Because little variation exists, little change in Hardy-Weinberg equilibrium occurs by splitting the individuals into more and more populations and so the program chooses this as the least costly place to introduce an additional cluster. Clearly this doesn't make biological sense, so in this case I'd say K=3 provides the best fit to the data.

Wiki Sandbox

2009-06-18 06:25:31

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- = Test Heading =	+ = State Links =

Wiki Sandbox

2009-06-18 06:25:11

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- [[TableOfContents]]	+ State response

Front Page

2009-06-11 08:26:49

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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

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

Wiki Sandbox

2009-06-07 22:34:32

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- Oh my GOD I'M BEING ATTACKED BEARS!	+ BEING ATTACKED BEARS!

Structurama

BobThomson — 2009-06-04 06:36:52

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	+ ------ + ''2009-06-04 07:36:52'' [[nbsp]] Thanks for pointing this out. The website has moved to this address http://fisher.berkeley.edu/structurama/. John Huelsenbeck recently posted an update on the new version of the program [http://treethinkers.blogspot.com/2009/05/programs-gone-awol-structurama.html?showComment=1243866025770#c1409363696610850262 here] --["Users/BobThomson"]

Structurama

BobThomson — 2009-06-04 06:33:58

url update

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- \|\|[http://www.structurama.org/index.html Structurama]\|\|	+ \|\|[http://fisher.berkeley.edu/structurama/ Structurama]\|\|

Phylogenetic Comparative Methods

BobThomson — 2009-06-04 06:32:21

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- ["Phylogenetics and Comparative Method in R"]: Examining Trait Evolution in ''Anolis'' Lizards!	+ ["Phylogenetics and Comparative Method in R"]: Examining Trait Evolution in ''Anolis'' Lizards.

Phylogenetic Comparative Methods

2009-06-04 00:21:12

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- ["Phylogenetics and Comparative Method in R"]: Examining Trait Evolution in ''Anolis'' Lizards	+ ["Phylogenetics and Comparative Method in R"]: Examining Trait Evolution in ''Anolis'' Lizards!

Structurama

2009-06-02 12:51:43

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	+ ------ + ''2009-06-02 13:51:43'' [[nbsp]] Dear Sir, + The software "Structurama" is not available anymore as The link "http://www.structurama.org/index.html" is not working anymore. + Best regards. + JL legras legras@colmar.inra.fr + + --79.93.189.182

Community Phylogenetics

zhang — 2009-04-29 18:42:38

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- We recommend saving the commands you type to a text file so that you have a record of your analyses. By cutting and pasting your text file into [http://www.phylodiversity.net/phylocom/ Phylocom] your analysis can also be easily replicated. We also recommend annotating this file with notes about what you've done and why. Open a new text file now in [http://www.barebones.com/products/TextWrangler/download.html TextWrangler]. Save your text file witht the name "Phylocom_Commands".	+ We recommend saving the commands you type to a text file so that you have a record of your analyses. By cutting and pasting your text file into [http://www.phylodiversity.net/phylocom/ Phylocom] your analysis can also be easily replicated. We also recommend annotating this file with notes about what you've done and why. Open a new text file now in [http://www.barebones.com/products/TextWrangler/download.html TextWrangler]. Save your text file with the name "Phylocom_Commands".

Parsimony (PAUP*)

BobThomson — 2009-04-28 07:36:57

minor edit

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- PAUP* should display a summary of the search along with a table of the results.	+ '''7.''' PAUP* should display a summary of the search along with a table of the results.

Parsimony (PAUP*)

BobThomson — 2009-04-28 07:35:26

Revert to version 11 (fixing recent minor edit. Was this an error?).

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Parsimony (PAUP*)

BobThomson — 2009-04-28 07:35:18

Revert to version 11 (fixing recent minor edit. Was this an error?).

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- '''7.'''PAUP* should display a summary of the search along with a table of the results.	+ PAUP* should display a summary of the search along with a table of the results.

Parsimony (PAUP*)

zhang — 2009-04-28 02:49:09

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- 7 PAUP* should display a summary of the search along with a table of the results.	+ '''7.'''PAUP* should display a summary of the search along with a table of the results.

Parsimony (PAUP*)

zhang — 2009-04-28 02:46:56

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- PAUP* should display a summary of the search along with a table of the results.	+ 7 PAUP* should display a summary of the search along with a table of the results.

Community Phylogenetics

2009-04-16 02:14:34

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	+ ------ + ''2009-04-16 03:14:34'' [[nbsp]] When species names are recorded per plot, how should we present them before starting the run? Kowiyouyessoufou1@gmail.com --152.106.240.10

Community Phylogenetics

2009-04-16 02:12:58

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	+ ------ + ''2009-04-16 03:12:58'' [[nbsp]] When species names are collected per plot, how should we present them so that they will be suitable for Phylocom? --152.106.240.10

Structure

2009-04-14 07:59:37

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	+ ------ + ''2009-04-14 08:59:37'' [[nbsp]] Dear Sir, + First thank you for this more explanation but could you please help me how to prepare an Input file for microsatelite data with 82 genotypes using 10 loci, especially that the 82 genotupes of almond (diploid) are divided into 5 different geographic origine because i have some troubles with Structure. + Thanks in advance + I'm Hassouna from Tunisia (North Africa) + My mail is zallaouz@yahoo.fr --196.203.116.113

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

Ancestral reconstruction and phylogenetic signal of discrete traits in Mesquite

2009-04-09 01:34:44

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	+ ------ + ''2009-04-09 02:34:44'' [[nbsp]] i would want to learn more --137.158.152.206

Community Phylogenetics

BobThomson — 2009-03-27 12:52:08

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- You should see a welcome screen that looks something like this [[Image(Figure1.jpg)]]	+ You should see a welcome screen that looks something like this + + [[Image(Figure1.jpg)]]

Generating Species Trees with BEST

BobThomson — 2009-03-27 07:47:21

(quick edit)

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	+ Note: This seems to work only if the tree is in a nexus formatted file. See the comments at the bottom of this tutorial if you are trying to do something else. +

Generating Species Trees with BEST

BobThomson — 2009-03-27 07:26:18

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	+ ------ + ''2009-03-27 08:26:18'' [[nbsp]] Interesting. I'm not quite sure whats going on here. It works fine as a nexus tree file, but not as a newick. So if you simply replace the '#'s in the .con nexus file that you get back from the sumt command, it should work. If you extract that tree, and put it in its own file, you'd want to do something like what you suggest. Thanks for pointing it out! I'll add a note in the text above. --["Users/BobThomson"]

Generating Species Trees with BEST

2009-03-26 17:57:44

Comment added.

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	+ ------ + ''2009-03-26 18:57:44'' [[nbsp]] I don't think + (O:0.018476,((H:0.008843,C:0.008843)0.67:0.000356[&theta=0.000998],G:0.009199)1.00:0.009277[&theta=0.004647]) + works. You need to use something like + (O:0.018476,((H:0.008843,C:0.008843)[&theta=0.000998]:0.000356,G:0.009199)[&theta=0.004647]:0.009277); --118.90.62.121

Front Page

GregPauly — 2009-03-24 18:00:19

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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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	+ -----

III. Loading Character Data into R

glor — 2009-03-24 07:51:11

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- '''d.''' Now let's add scale bars that indicate the size of each species to this tree. The way we're going to do this is by telling R to make {{{segments}}} at the tips of our tree that scale with body size.	+ '''d.''' Now let's add scale bars that indicate the size of each species to this tree. The way we're going to do this is by telling R to make {{{segments}}} at the tips of our tree that scale with body size. The {{{segments}}} command works by connecting points in R's X/Y coordinate space with a line, or segment. We're going to use this command to make a series of lines connecting two points using the following command:
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	+ This command is broken down into three parts: (1) starting X coordinates, (2) starting Y coordinates, (3) ending X coordinates, (4) ending Y coordinates. The first part of this command {{{rep(101.5,85)}}} uses the {{{rep}}} command to generate a vector that contains the value {{{101.5}}} repeated 85 times. We're doing this because we want to create a line for each of the 85 taxa in our tree, and we want all of these lines to start at an x-value of {{{101.5}}} (you may find that you need to adjust this value on a case-by-case basis to make the lines appear where you want them relative to the tips of your tree). The next command {{{1:85}}} tells R that we want lines to begin at integer values ranging from 1-85 on the Y axis: by convention, the tips of phylogentic trees are found at integer values along the Y axis. The next part of this command {{{rep(101.5,85) + SVL[anolisComparativeTree$tip.label]}}}} tells R how far lines will extend along the X-axis, in this case, they're going to be as long as the SVL value for the species in our dataset. The final part tells R that our segmets will be horizontal lines by repeating the vector with integer values ranging from 1 to 85 for the final Y coordinates of each line. + +

III. Loading Character Data into R

YStuart — 2009-03-23 12:18:19

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- {{{ >segments(rep(76.5,85), 1:85, rep(76.5,85) + SVL[anolisComparativeTree$tip.label], 1:85, lwd=2)}}}	+ {{{ >segments(rep(101.5,85), 1:85, rep(101.5,85) + SVL[anolisComparativeTree$tip.label], 1:85, lwd=2)}}}

III. Loading Character Data into R

YStuart — 2009-03-23 12:17:41

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- {{{points(rep(75.5, length(anolisComparativeTree$tip.label)), 1:length(anolisComparativeTree$tip.label), pch=22, bg=microLabel[anolisComparativeTree$tip.label], cex=0.5, lwd=0.25)}}}	+ {{{points(rep(100.5, length(anolisComparativeTree$tip.label)), 1:length(anolisComparativeTree$tip.label), pch=22, bg=microLabel[anolisComparativeTree$tip.label], cex=0.5, lwd=0.25)}}}

II. Tree Basics

2009-03-23 10:46:06

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- Numerous relaxed clock methods are available. Only one such method is implemented in R: Sanderson's non-parametric rate smoothing (NPRS). If you require a quick and dirty ultrametric tree you can use the {{{chronogram}}} function of {{{ape}}} to get render a non-ultrametric tree ultrametric using NPRS. Other, more recently-developed methods like Sanderson's penalized-likelihood (PL) method and the Bayesian approach implemented by BEAST are superior to NPRS. Even if you want to make a tree ultrametric using NPRS you should use Sanderson's r8s program instead of {{{chronogram}}} in R because it offer a suite of diagnostics that will ensure nothing goes horribly wrong.	+ Numerous relaxed clock methods are available. Only one such method is implemented in R: Sanderson's non-parametric rate smoothing (NPRS). If you require a quick and dirty ultrametric tree you can use the {{{chronogram}}} function of {{{ape}}} to get render a non-ultrametric tree ultrametric using NPRS. Other, more recently-developed methods like Sanderson's penalized-likelihood (PL) method and the Bayesian approach implemented by BEAST are superior to NPRS. Even if you want to make a tree ultrametric using NPRS you should use Sanderson's r8s program instead of {{{chronogram}}} in R because it offers a suite of diagnostics that will ensure nothing goes horribly wrong.

II. Tree Basics

2009-03-23 10:37:44

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- Before going any further, we need to start learning how R stores and builds trees. This is absolutely essential if we’re going to learn how to take full advantage of R and eventually write our own functions to exploit R’s potential. Instead of storing each tree as a single line of text (as is the case with NEWICK formatted trees), R stores trees as objects consisting of several distinct components. Multipart objects stored in this manner in R are referred to as ‘lists.‘ There are several different ways of storing tree in R. So far, we’ve been working with the most widely-used format, which is called the ‘phylo’ format. This tree format was created by Paradis for his Ape package. If we type ‘help(read.nexus)’ we can see the components that make up a ‘phylo’ formatted tree file R - they’re listed under the Value heading: edge, edge.length, tip.label, node.label, and root.edge.	+ Before going any further, we need to start learning how R stores and builds trees. This is absolutely essential if we’re going to learn how to take full advantage of R and eventually write our own functions to exploit R’s potential. Instead of storing each tree as a single line of text (as is the case with NEWICK formatted trees), R stores trees as objects consisting of several distinct components. Multipart objects stored in this manner in R are referred to as ‘lists.‘ There are several different ways of storing trees in R. So far, we’ve been working with the most widely-used format, which is called the ‘phylo’ format. This tree format was created by Paradis for his Ape package. If we type ‘help(read.nexus)’ we can see the components that make up a ‘phylo’ formatted tree file R - they’re listed under the Value heading: edge, edge.length, tip.label, node.label, and root.edge.

II. Tree Basics

2009-03-23 10:27:23

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- You’re getting this error because you haven’t yet told R the location of the file you’d like to open. R doesn’t search your entire hard drive for a particular file, it only searches in the folder that is active as its working directory. Before you can load your tree, you need to tell R which directory you’ll be working from. To do this you simply go to the ‘Misc’ menu, select ‘Change working directory...’, and choose the desired location (For this to work you need to actually click open the folder you’d like be working in before clicking the Open button in R: if you just click on the name of the folder you’d like to work from and click Open you may end up in the directory above the one you’d actually like to be in). After you’ve selected the appropriate directory, try running the read.nexus line above a second time. If you get another R prompt after hitting return, you’re ready to move on to step 2.	+ You’re getting this error because you haven’t yet told R the location of the file you’d like to open. R doesn’t search your entire hard drive for a particular file, it only searches in the folder that is active as its working directory. Before you can load your tree, you need to tell R which directory you’ll be working from. To do this you simply go to the ‘Misc’ menu, select ‘Change working directory...’, and choose the desired location (For this to work you need to actually click open the folder you’d like to be working in before clicking the Open button in R: if you just click on the name of the folder you’d like to work from and click Open you may end up in the directory above the one you’d actually like to be in). After you’ve selected the appropriate directory, try running the read.nexus line above a second time. If you get another R prompt after hitting return, you’re ready to move on to step 2.

2009 Bodega Bay Photo Gallery

CathyNewman — 2009-03-23 08:33:58

Group pic!!

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	+ \|\|[[Image(group.jpg, 500, thumbnail, noborder)]]\|\| + ===

2009 Bodega Bay Photo Gallery

CathyNewman — 2009-03-23 08:32:20

Upload of image group.jpg.

Divergence Time Estimation (Moore)

2009-03-22 11:24:12

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- There will be a one hour lecture to provide an overview of various methods for inferring divergence times, followed by a one hour tutorial for estimating divergence times using BEAST.	+ There will be a 1.5 hour lecture to provide an overview of various methods for inferring divergence times, followed by a 1.5 hour tutorial for estimating divergence times using BEAST.

4. Specifying a Starting Tree

2009-03-21 17:53:55

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- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], as well as in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.

1. Overview of the Analysis Pipeline

2009-03-21 14:13:17

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- Our tutorial on "estimating divergence times from molecular sequence data" with BEAST continues ["2. Formatting XML Input File with BEAUti" here].	+ Our tutorial on "estimating divergence times from molecular sequence data" with BEAST continues ["2. Formatting BEAST Input Files" here].

1. Overview of the Analysis Pipeline

2009-03-21 14:12:24

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	+ + Our tutorial on "estimating divergence times from molecular sequence data" with BEAST continues ["2. Formatting XML Input File with BEAUti" here].

4. Specifying a Starting Tree

2009-03-21 14:07:47

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- The preceding steps provide a chronogram that can be used as a starting tree in our XML file.	+ The preceding steps provide a chronogram that can now be used as a starting tree in our XML file.

4. Specifying a Starting Tree

2009-03-21 14:07:03

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- i. Now open the file that we generated with TreeEdit in TextWrangler. Select and copy the first tree in the NEXUS file, as depicted below.	+ i. In TextWrangler, open the file that we previously generated with TreeEdit. Select and copy the first tree in the NEXUS file, as depicted below.

4. Specifying a Starting Tree

2009-03-21 14:05:13

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	+ The preceding steps provide a chronogram that can be used as a starting tree in our XML file. +
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- The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. - i. Add a {{{‘newick’}}} tree element to the XML file.	+ We are now ready to specify the starting tree in the XML file with the following steps. + i. Using TextWrangler, add a {{{‘newick’}}} element to the XML file, as depicted below.
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- i. Open the NPRS starting tree in a text editor, then select and copy the first tree in the NEXUS file.	+ i. Now open the file that we generated with TreeEdit in TextWrangler. Select and copy the first tree in the NEXUS file, as depicted below.
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- i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element.	+ i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element, as depicted below.
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- i. Modifying the treeModel element {{{‘ text here’}}}.	+ i. Finally, specify {{{‘newick’}}} as the starting tree in the first line of the {{{‘treeModel’}}} element, as depicted below.

4. Specifying a Starting Tree

2009-03-21 13:55:50

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- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.

4. Specifying a Starting Tree

2009-03-21 13:51:58

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- i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. These options are depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}}. These options are depicted below.
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- i. The tree has now been rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.	+ i. After clicking on the {{{‘OK’}}} button, the tree will be rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.

4. Specifying a Starting Tree

2009-03-21 13:50:40

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- i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. You should see that the tree becomes ultrametric (i.e., such that the distance from the root to each tip is equal), as depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. These options are depicted below.
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- i. Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.	+ i. The tree has now been rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.

4. Specifying a Starting Tree

2009-03-21 13:47:59

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- i. With the cursor tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.	+ i. With the 'cursor' tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.
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- i. Select the rooting tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}.	+ i. Select the 'rooting' tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}. You should see that the tree becomes rooted along the selected branch, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. You should see that the tree becomes ultrametric (i.e., such that the distance from the root to each tip is equal), as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Press and hold down on the 'node information' tool to display the list of options, and then scroll down to select the {{{‘Node heights’}}} option, which will display the height of the internal nodes in expected number of substitutions, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. With the cursor tool, select the branch that is sister to {{{‘Platanus_kerrii’}}}, (i.e., the branch subtending the clade that includes {{{‘Platanus_orientalis’}}}, {{{‘Platanus_racemosa’}}}, {{{‘Platanus_maxicana’}}}, and {{{‘Platanus_occidentalis’}}}). You should see that the selected clade is now highlighted, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. From the '''Trees''' menu, select the {{{‘Scale tree...’}}} option. A window will appear listing several options: click the {{{‘Scale To:’}}} button, then select the {{{‘Scale selected height to:’}}} button, and type the value {{{‘50.0’}}} in the adjacent window (this value falls within the range that we previously specified for the age of this clade in our XML file). Next, click {{{‘OK’}}}. You should see that ages of all the remaining nodes in the tree are scaled accordingly, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. From the '''File''' menu, select the {{{‘Export...’}}} option. An {{{‘Export Tree(s)’}}} window will appear listing several options: click to de-select the {{{‘Use Translation List for Taxon Names’}}} button, and then click {{{‘OK’}}}. An {{{‘Export Data File’}}} window will appear: specify the name and location of the tree file, and then click {{{‘OK’}}}, as depicted below.

4. Specifying a Starting Tree

2009-03-21 13:21:18

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- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files available ["Divergence Time Estimation (Moore)" here].	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the example data files available ["Divergence Time Estimation (Moore)" here].
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- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.
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- i. Comment out the {{{‘constantSize’}}} element as depicted below.	+ i. Double click on the TreeEdit icon to launch the application. From the '''File''' menu, select the {{{‘Open...’}}} option, and navigate to the directory that contains the file {{{‘Platanus_con_tree.tre’}}}. + + i. With the cursor tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the rooting tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}.

4. Specifying a Starting Tree

2009-03-21 13:11:01

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- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program [[File(TreeEdit.zip)]].	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit. +

4. Specifying a Starting Tree

2009-03-21 13:09:10

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4. Specifying a Starting Tree

2009-03-21 13:09:04

Upload of file TreeEdit.zip.

4. Specifying a Starting Tree

2009-03-21 13:08:11

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- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files available ["Divergence Time Estimation (Moore)" here]. + + We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program [[File(TreeEdit.zip)]].

4. Specifying a Starting Tree

2009-03-21 13:04:06

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- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["#nprs" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 13:03:38

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- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics#nprs" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["#nprs" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 13:02:47

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- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics#nprs" elsewhere] in this wiki. TreeEdit

II. Tree Basics

2009-03-21 12:57:49

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-	+ [[Anchor(nprs)]]

4. Specifying a Starting Tree

2009-03-21 12:54:52

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- This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis, which is included in the in the example data files for the tutorial) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.	+ This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.
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- The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process.	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 11:49:52

(quick edit)

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- ===== '''Ready to roll! (Finally) ''' =====	+ ===== '''Ready to roll! (At last!) ''' =====

3. Editing XML Input File

2009-03-21 11:42:41

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial.

2. Formatting BEAST Input Files

2009-03-21 11:42:21

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- Click the {{{‘Generate BEAST file’}}} in the lower right hand corner of the BEAUti window, and save the generated file as {{{‘Platanus_DTE.xml’}}}. Congratulations, you are half way there!! Now we need to make some manual modifications to our newly generated 'base' XML file, which we will describe in the ["3. Editing XML Input File" next tutorial].	+ Click the {{{‘Generate BEAST file’}}} in the lower right hand corner of the BEAUti window, and save the generated file as {{{‘Platanus_DTE.xml’}}}. Congratulations, you are half way there!! Now we need to make some manual modifications to our newly generated 'base' XML file, which we will describe in the ["3. Editing XML Input File" next] part of the tutorial.

3. Editing XML Input File

2009-03-21 11:42:04

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- What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next tutorial].	+ What gives? As suggested by the error message, BEAST is attempting to initiate the MCMC from a randomly generated starting tree that violates the temporal and/or topological constraints that we have just defined, which is described in the error message as an {{{‘initial state is incompatible with one or more 'hard' constraints (on monophyly or bounds on parameter values)’}}}. Moreover, the error message specifically identifies the culprit--{{{‘clade1_constraint=-Inf’}}}--indicating that the {{{'clade1_constraint'}}} has been violated and caused the initial state of the chain to have a likelihood of negative infinity. The solution to this problem is to specify a starting tree that satisfies the temporal and topological constraints that we have imposed, which we will describe in the ["4. Specifying a Starting Tree" next] part of the tutorial

4. Specifying a Starting Tree

2009-03-21 11:35:31

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- ==== - ii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - iii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - iv. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - v. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - vi. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - vii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- ==== - viii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 11:34:22

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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ iii. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ iv. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ v. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ vi. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ vii. Comment out the {{{‘coalescentTree’}}} element as depicted below.
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- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ viii. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 11:31:52

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	+ + ===== + ===== '''Ready to roll! (Finally) ''' ===== + We're finally ready to initiate the BEAST analysis, which we will describe in the ["5. Running a BEAST Analysis" next] part of the tutorial.

4. Specifying a Starting Tree

2009-03-21 11:28:48

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2009-03-21 11:28:40

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- \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|	+ \|\|<:>[[Image(starting_tree.png, thumbnail, 650, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-21 11:20:55

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- ==== - i. Comment out the {{{‘coalescentTree’}}} element as depicted below. - \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|
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- i. Copy the NPRS chronogram into the {{{‘newick’}}} tree element.	+ i. Open the NPRS starting tree in a text editor, then select and copy the first tree in the NEXUS file. + \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\| + i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element.

4. Specifying a Starting Tree

2009-03-21 11:17:40

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2009-03-21 11:16:15

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4. Specifying a Starting Tree

2009-03-21 11:15:44

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- ===== '''Step 2: Title for step 2''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_2.png, thumbnail, 500, noborder)]]\|\|	+ ===== '''Step 2: Preparing a user-specified starting tree''' ===== + The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. + i. Comment out the {{{‘constantSize’}}} element as depicted below. + \|\|<:>[[Image(tree_1.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_2.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_3.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_5.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_6.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_7.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_8.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_9.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|
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- ===== '''Step 3: Title for step 3''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_3.png, thumbnail, 555, noborder)]]\|\| - - ==== - ===== '''Step 4: Title for step 4''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_5.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== Step 5: Title for step 5 ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_6.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 6: Title for step 6''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_7.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 7: Title for step 7''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_8.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 8: Title for step 8''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_9.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 9: Title for step 9''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== Specifying a starting tree ===== - How to enforce the monophyly of a specified clade {{{‘text here’}}}. - i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| - i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| - i. Specifying a newick tree element {{{‘ text here’}}}.	+ ===== '''Step 3: Adding the user-specified starting tree to the XML file''' ===== + The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. + i. Add a {{{‘newick’}}} tree element to the XML file. + \|\|<:>[[Image(newick_1.png, noborder)]]\|\| + i. Copy the NPRS chronogram into the {{{‘newick’}}} tree element.

4. Specifying a Starting Tree

2009-03-21 11:08:17

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- This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.	+ This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis, which is included in the in the example data files for the tutorial) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.

4. Specifying a Starting Tree

2009-03-21 11:07:03

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- The XML file generated by BEAUti will include commands to generate a random starting tree using a coalescent process. The phylogeny generated under the coalescent process is likely to violate the temporal and/or topological constraints used for calibration, which will cause an error when we initiate the MCMC. Accordingly, we will ensure that the commands for generating a coalescent tree are ignored by BEAST, which could be achieved by simply removing these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, and can contain any characters except {{{--}}}. - i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}.	+ The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. These random starting trees are very likely to violate the temporal and/or topological constraints that we specified to calibrate divergence times, and will therefore cause an error when we attempt initiate the MCMC. Accordingly, we will ensure that BEAST will ignore the commands for generating a random coalescent tree, which could be achieved either by deleting these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, such that everything between these two tokens is ignored when the program is executed. There are two elements in the XML file that need to be commented out; the {{{‘constantSize’}}} and {{{‘coalescentTree’}}} elements. + i. Comment out the {{{‘constantSize’}}} element as depicted below.
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- i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}.	+ i. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 10:47:00

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- ===== '''Step 1: Title for step 1''' ===== - The first step {{{‘text here’}}}. - \|\|<:>[[Image(tree_1.png, thumbnail, 500, noborder)]]\|\|	+ ===== '''Step 1: Commenting out the default starting tree''' ===== + The XML file generated by BEAUti will include commands to generate a random starting tree using a coalescent process. The phylogeny generated under the coalescent process is likely to violate the temporal and/or topological constraints used for calibration, which will cause an error when we initiate the MCMC. Accordingly, we will ensure that the commands for generating a coalescent tree are ignored by BEAST, which could be achieved by simply removing these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, and can contain any characters except {{{--}}}. + i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| + i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block2.png, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-21 10:29:40

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- This tutorial describes how to specify a starting tree for the MCMC that satisfies the temporal and topological constraints that we specified in Step 3 of the tutorial.	+ In the previous tutorial we described how to impose constraints within the XML file that collectively provide a means of calibrating divergence times. Here, we describe how to specify a starting tree for the MCMC that satisfies those temporal and topological constraints. + + This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file. + + Open the edited XML file in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the XML file.

2. Formatting BEAST Input Files

2009-03-21 10:07:38

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- Click the {{{‘Generate BEAST file’}}} in the lower right hand corner of the BEAUti window, and save the generated file as {{{‘Platanus_DTE.xml’}}}. Congratulations, you are half way there!!	+ Click the {{{‘Generate BEAST file’}}} in the lower right hand corner of the BEAUti window, and save the generated file as {{{‘Platanus_DTE.xml’}}}. Congratulations, you are half way there!! Now we need to make some manual modifications to our newly generated 'base' XML file, which we will describe in the ["3. Editing XML Input File" next tutorial].

4. Specifying a Starting Tree

2009-03-21 10:02:40

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	+ ====
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- ===== Step 6: Title for step 6 =====	+ ==== + ===== '''Step 6: Title for step 6''' =====
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- ===== Step 7: Title for step 7 =====	+ ==== + ===== '''Step 7: Title for step 7''' =====
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- ===== Step 9: Title for step 9 =====	+ ==== + ===== '''Step 9: Title for step 9''' =====
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	+ ====

1. Overview of the Analysis Pipeline

2009-03-21 09:48:09

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- ===== Step I: Multiple Sequence Alignment=====	+ ===== '''Step I: Multiple Sequence Alignment''' =====
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- ===== Step II: Selecting a Model of Nucleotide Substitution=====	+ ===== '''Step II: Selecting a Model of Nucleotide Substitution''' =====
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- ===== Step III: Assessing the Level of Substitution Rate Variation=====	+ ===== '''Step III: Assessing the Level of Substitution Rate Variation''' =====
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- ===== Step IV: Estimating Phylogeny Under Candidate Partition Schemes=====	+ ===== '''Step IV: Estimating Phylogeny Under Candidate Partition Schemes''' =====
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- ===== Step V: Estimating Divergence Times Under the Selected Mixed-Model=====	+ ===== '''Step V: Estimating Divergence Times Under the Selected Mixed-Model''' =====

3. Editing XML Input File

2009-03-21 09:46:14

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- ===== Step 1: Defining a clade =====	+ ==== + ===== '''Step 1: Defining a clade''' =====
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- ===== Step 2: Monitoring the monophyly of the specified clade =====	+ ==== + ===== '''Step 2: Monitoring the monophyly of the specified clade''' =====
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- ===== Step 3: Monitoring the age of the specified clade =====	+ ==== + ===== '''Step 3: Monitoring the age of the specified clade''' =====
Line 25:	Line 28:
- ===== Step 4: Enforcing the monophyly of the specified clade =====	+ ==== + ===== '''Step 4: Enforcing the monophyly of the specified clade''' =====
Line 33:	Line 37:
- ===== Step 5: Calibrating the age of the specified clade =====	+ ==== + ===== '''Step 5: Calibrating the age of the specified clade''' =====
Line 40:	Line 45:
- ===== Almost (but not quite) ready to roll... =====	+ ===== '''Almost (but not quite) ready to roll...''' =====

2. Formatting BEAST Input Files

2009-03-21 09:44:41

Differences for 2. Formatting BEAST Input Files

Deletions are marked with - .	Additions are marked with +.
Line 10:	Line 10:
	+ ====
Line 15:	Line 16:
	+ ====
Line 20:	Line 22:
	+ ====
Line 31:	Line 34:
	+ ====
Line 40:	Line 44:
	+ ====
Line 51:	Line 56:
	+ ====
Line 56:	Line 62:
	+ ====
Line 66:	Line 73:
	+ ====

2. Formatting BEAST Input Files

2009-03-21 09:43:38

Differences for 2. Formatting BEAST Input Files

Deletions are marked with - .	Additions are marked with +.
Line 10:	Line 10:
- ===== Step 1: Getting a NEXUS file into BEAUti =====	+ ===== '''Step 1: Getting a NEXUS file into BEAUti''' =====
Line 15:	Line 15:
- ===== Step 2: The data window =====	+ ===== '''Step 2: The data window''' =====
Line 20:	Line 20:
- ===== Step 3: Defining groups of taxa ====	+ ===== '''Step 3: Defining groups of taxa''' ====
Line 31:	Line 31:
- ===== Step 4: Model specification =====	+ ===== '''Step 4: Model specification''' =====
Line 40:	Line 40:
- ===== Step 5: Prior specification =====	+ ===== '''Step 5: Prior specification''' =====
Line 51:	Line 51:
- ===== Step 6: Proposal mechanisms =====	+ ===== '''Step 6: Proposal mechanisms''' =====
Line 56:	Line 56:
- ===== Step 7: MCMC =====	+ ===== '''Step 7: MCMC''' =====
Line 66:	Line 66:
- ===== Step 8: Generate the xml file! =====	+ ===== '''Step 8: Generate the xml file!''' =====