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Preprint

Phylogenetics

AD Adrián A. Davín
PH Philip Hugenholtz
GS Gergely J. Szöllősi
TW Tom A. Williams

Last updated date: Sep 13, 2022 Views: 558 Forks: 0

original An abbreviated version of this protocol was published in Science in May, 2021
A rooted phylogeny resolves early bacterial evolution
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Hi Alberto,

 

the species tree file (rooted in 3 different places --- the "root region") is available in the FigShare repository for the paper here: https://doi.org/10.6084/m9.figshare.12651074.v12

 

However, the tips correspond to some short codes we used during the analyses. A "conversion table" with metadata for each short code is also in the FigShare repository, but to save any trouble, I have relabelled the "root 528" tree with the full taxonomy string (see the attached ZIP archive, which contains the original tree, metadata file, relabelled species tree and code for relabelling). The root position is unlikely to be critical for preparing a figure showing the distribution of a protein family, but you could reroot on the other adjacent branches of the root region if you wish.

 

The relabelling script is very straightforward, so if you want to use only the species name (or similiar), the code can be easily modified to do so. 

 

All the best,

 

Tom

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Davín, A, Hugenholtz, P, Szöllősi, G and Williams, T(2022). Phylogenetics. Bio-protocol Preprint. bio-protocol.org/prep1923.
  2. Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J. and Williams, T. A.(2021). A rooted phylogeny resolves early bacterial evolution. Science 372(6542). DOI: 10.1126/science.abe0511

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