Recent Changes for "Links" - Bodega Phylogenetics Wiki

Links

glor — 2009-03-13 13:19:47

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	+ + [http://www.r-phylo.org/wiki/Main_Page R-Phylo Wiki] + A great place for additional help with R and associated phylogenetic applications.

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glor — 2008-04-29 09:59:00

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- The Cipres Portal is a computational resource for analysis of large phylogenetic datasets. You can submit your dataset through the portal and have it analyzed at the [http://www.sdsc.edu/ San Diego Supercomputer Center]. Methods currently available on the portal (as of April 29, 2008) include parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), Bayesian inference (MrBayes). Implementation of some analyses remains somewhat buggy or restrictive. For example, partitioned analyses are not permitted with MrBayes. Moreover, input parameters for Bayesian analyses must be submitted via the web interface rather than being imbedded in the input file.	+ The Cipres Portal is a computational resource for analysis of large phylogenetic datasets. You can submit your dataset through the portal and have it analyzed at the [http://www.sdsc.edu/ San Diego Supercomputer Center]. Methods currently available on the portal (as of April 29, 2008) include parsimony (the ratchet and Rec-I-DCM3), maximum likelihood ([http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm RAxML] and [http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html GARLI]), Bayesian inference ([http://mrbayes.csit.fsu.edu/ MrBayes]). Implementation of some analyses remains somewhat buggy or restrictive. For example, partitioned analyses are not permitted with MrBayes. Moreover, input parameters for Bayesian analyses must be submitted via the web interface rather than being imbedded in the input file.

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glor — 2008-04-29 09:57:27

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- The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is still a little buggy).	+ The Cipres Portal is a computational resource for analysis of large phylogenetic datasets. You can submit your dataset through the portal and have it analyzed at the [http://www.sdsc.edu/ San Diego Supercomputer Center]. Methods currently available on the portal (as of April 29, 2008) include parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), Bayesian inference (MrBayes). Implementation of some analyses remains somewhat buggy or restrictive. For example, partitioned analyses are not permitted with MrBayes. Moreover, input parameters for Bayesian analyses must be submitted via the web interface rather than being imbedded in the input file.
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- Joe Felsenstein has compiled an impressive list of available software that performs various phylogenetic tasks. This is BY FAR the most comprehensive such list I'm aware of, if you're looking for any software having to do with phylogenetics, it's likely that it's listed here.	+ Joe Felsenstein has compiled an impressive list of available software that performs various phylogenetic tasks. This is the most comprehensive such list we're aware of; if you're looking for any software having to do with phylogenetics, it's likely that it's listed here.

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BobThomson — 2008-02-29 14:35:41

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- [http://www.nescent.org/index.php NESCent] - The National Evolutionary Synthesis Center's webpage.	+ [http://www.nescent.org NESCent], the National Evolutionary Synthesis Center, is an NSF-sponsored research center in Durham, NC. It offers postdoc positions, facilities and grants for various kinds of meetings, information technology support, education & outreach, sabbaticals, and more.

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2008-02-27 08:48:29

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- [http://evolution.genetics.washington.edu/phylip/software.html iTOL]	+ [http://itol.embl.de/ iTOL]

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2008-02-27 08:47:47

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- [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite Manual] ''Appears to be down at the moment - RCT 2/23''	+ [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite Manual]

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2008-02-27 08:47:07

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- BML's website. Contains lots of information about the reserve. For info about housing, go [http://www-bml.ucdavis.edu/housing/index.html here].	+ BML's website. Contains lots of information about the reserve. For info about housing, go [http://www-bml.ucdavis.edu/housing/housinginfo.html here].

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2008-02-27 08:43:59

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- BML's website. Contains lots of information about the reserve.	+ BML's website. Contains lots of information about the reserve. For info about housing, go [http://www-bml.ucdavis.edu/housing/index.html here].

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2008-02-27 08:43:07

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- Mike Sanderson's database of genbank derived clusters.	+ Mike Sanderson's database of Genbank-derived clusters.

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BobThomson — 2008-02-25 18:24:33

eegads...how could I forget the phylota browser!

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	+ [http://loco.biosci.arizona.edu/pb/ Phylota browser] + Mike Sanderson's database of genbank derived clusters. +

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BCOMeara — 2008-02-23 19:36:33

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- Joe Felsenstein has compiled an impressive list of available software that performs various phylogenetic tasks. This is BY FAR the most comprehensive such list I'm aware of, if you're looking for any software having to do with phylogenetics, its likely that its listed here.	+ Joe Felsenstein has compiled an impressive list of available software that performs various phylogenetic tasks. This is BY FAR the most comprehensive such list I'm aware of, if you're looking for any software having to do with phylogenetics, it's likely that it's listed here.

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BobThomson — 2008-02-23 11:37:53

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- The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).	+ The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is still a little buggy).

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BobThomson — 2008-02-23 11:37:24

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- The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).	+ The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (the ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).

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BobThomson — 2008-02-23 11:37:09

(quick edit)

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- The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods including maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).	+ The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods include maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).

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BobThomson — 2008-02-23 11:36:57

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- The Cipres Portal provides servers to carry out several phylogenetics inference methods (particularly methods for analyzing large datasets). Available methods including maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).	+ The Cipres Portal provides servers to carry out several phylogenetic inference methods (particularly methods for analyzing large datasets). Available methods including maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still).

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BobThomson — 2008-02-23 11:36:28

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- ==Other random links==	+ ==Other==

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BobThomson — 2008-02-23 10:30:26

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- [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite Manual]	+ [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite Manual] ''Appears to be down at the moment - RCT 2/23''
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- - - - ''2008-02-23 10:20:47'' [[nbsp]] The Mesquite Webpage seems to be down at the moment. --["Users/BobThomson"]

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BobThomson — 2008-02-23 10:25:31

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- [[Comments]] - ------	+ +

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BobThomson — 2008-02-23 10:20:47

Comment added.

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	+ ------ + ''2008-02-23 10:20:47'' [[nbsp]] The Mesquite Webpage seems to be down at the moment. --["Users/BobThomson"]

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BobThomson — 2008-02-23 10:20:27

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	+ ==Phylogenetics== + [http://www.phylo.org/sub_sections/portal/ CIPRes Portal] + The Cipres Portal provides servers to carry out several phylogenetics inference methods (particularly methods for analyzing large datasets). Available methods including maximum parsimony (Ratchet and Rec-I-DCM3), maximum likelihood (RAxML and GARLI), bayes (MrBayes, though this implementation is a little buggy still). + + [http://evolution.genetics.washington.edu/phylip/software.html Felsenstein's List] + Joe Felsenstein has compiled an impressive list of available software that performs various phylogenetic tasks. This is BY FAR the most comprehensive such list I'm aware of, if you're looking for any software having to do with phylogenetics, its likely that its listed here. + + [http://evolution.genetics.washington.edu/phylip/software.html iTOL] + A pretty handy tree display webapp that allows various tree annotations. + + [http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/manual.html Mesquite Manual] + The online documentation for Mesquite. This often comes in handy when playing with some of Mesquite's myriad options and functions. + + ==Other random links== + [http://www-bml.ucdavis.edu/ Bodega Marine Lab] + BML's website. Contains lots of information about the reserve. + + [http://www.nescent.org/index.php NESCent] + The National Evolutionary Synthesis Center's webpage. + + [[Comments]]