How to read phylogenetic tree downloaded from ncbi taxonomy

[Chirag Parsania]

Hi,

I have downloaded phylogenetic tree from ncbi taxonomy database using ncbi taxonomy ids.  See the attachment. File extension of tree is .phy. When I try to read this in R using read.tree it changes tree labels to some weird symbols.  

Kindly let me know how can I load the tree in R and further play using ggtree ?

Also, once the tree loaded in the R, How can I convert tree to distance matrix ?

Thanks,

Chirag.

[Yu, Guangchuang]

treetext = readLines("phyliptree-5.phy")
treetext = paste0(treetext, collapse="")

read.tree(text=treetext)

the above commands work for your tree file which split newick tree text to more than 10k lines and should be pasted to a single line.

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G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. doi:10.1111/2041-210X.12628
 
Homepage: https://guangchuangyu.github.io/software/ggtree
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Guangchuang Yu PhD

Postdoc researcher
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

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