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If an article has a published phylogeny, is it common to get the newick file with branch lengths from the authors? In order to do further research with the tree.

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It is standard practice for authors to publish their trees on TreeBase for other people to use. They'll usually list the link in the supplementary material of the paper. Some journals made this a requirement for authors.

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  • $\begingroup$ @Ferroao I'm not sure what you mean, most of the trees on TreeBase have branch lengths $\endgroup$ – C_Z_ Feb 28 '17 at 19:59
  • $\begingroup$ I haven't seen much with branch lengths, as the ones i needed $\endgroup$ – Ferroao Feb 28 '17 at 20:03
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Look at the R script related to this article. rotl: an R package to interact with the Open Tree of Life data http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12593/full

install.packages("rotl")
library(rotl)
studies <- studies_find_studies(property = "ot:focalCladeOTTTaxonName", 
                                    value = "Caesalpinieae", exact = TRUE)
tree <- get_study_tree(study_id = studies[["study_ids"]][1],
                           tree_id = strsplit(studies[["tree_ids"]],", ")[[1]][1])

# Example 2
cat_studies <- studies_find_studies(property = "ot:focalCladeOTTTaxonName", 
value = "Felidae", exact = TRUE)
cat_tree <- get_study_tree(study_id = cat_studies[["study_ids"]][1],
tree_id = cat_studies[["tree_ids"]][1])
cat_tree
##
## Phylogenetic tree with 38 tips and 37 internal nodes.
##
## Tip labels:
## Neofelis_nebulosa, Panthera_tigris, Panthera_uncia, Panthera_pardus, ...
##
## Rooted; includes branch lengths.
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