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Phylogenetics in R

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Talk given on 18 Nov, 2011 on doing phylogenetics in R.

Technology
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Phylogenetics in R Scott Chamberlain November 18, 2011
What sorts of phylogenetics things can I do in R?
The run down ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Basic trees in R ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Get sequence data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Align sequence data run external: clustal, mafft ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object], Manual aligment may have to be done, dare I say it, not in R
Get and align sequences DIY ,[object Object],[object Object],[object Object],[object Object],[object Object]
Phylogenetic inference Tools ,[object Object],[object Object],[object Object]
Phylogenetic inference ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Phylogenetic inference---Continued ,[object Object],[object Object],[object Object]
Phylogenetic inference DIY ,[object Object],[object Object],[object Object],[object Object]
Visualize phylogenies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Visualize phylogenies DIY ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Traits on trees phylogenetic signal ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Traits on trees modeling trait evolution ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Ancestral state reconstruction ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Tree simulations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Get trees ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Phylogenetic community structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bonus: Polytomy resolver ,[object Object],[object Object],[object Object],[object Object],[object Object]
Resources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Phylogenetics in R

  • 1. Phylogenetics in R Scott Chamberlain November 18, 2011
  • 2. What sorts of phylogenetics things can I do in R?
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