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spholmes / F1000_workflow

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tree format? #41

Closed marwa38 closed 1 year ago

marwa38 commented 2 years ago

Hello

I created the tree using the workflow mentioned in https://f1000research.com/articles/5-1492 So could you please let me what is the format of the tree in that case? Is there is a function or something to know the format? if it is NEWICK, or etc

Thanks very much

spholmes commented 2 years ago

This is an object of class "phylo", see the description here: https://cran.r-project.org/web/packages/ape/ape.pdf or in the phangorn package, you can transform it to Newick or other formats using the ape function write.tree for instance

On Tue, Jan 4, 2022 at 6:33 AM marwa38 @.***> wrote:

Hello

I created the tree using the workflow mentioned in https://f1000research.com/articles/5-1492 So could you please let me what is the format of the tree in that case? Is there is a function or something to know the format? if it is NEWICK, or etc

Thanks very much

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marwa38 commented 2 years ago

thanks very much @spholmes that's helpful I transformed to Newick Do you recommend an app for visualising the tree? or just doing that in R? Is bootstrapping important for visualising?

spholmes commented 2 years ago

Just use either the R packages already available: ape or phangorn packages, or I like the ggtree package if your tree is not too big, best of luck

On Fri, Jan 7, 2022 at 12:15 PM marwa38 @.***> wrote:

thanks very much @spholmes https://github.com/spholmes that's helpful I transformed to Newick Do you recommend an app for visualising the tree? or just doing that in R? Is bootstrapping important for visualising?

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