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Implementation of the inference algorithm

RN Richard A Neher
BS Boris I Shraiman

Last updated date: Jul 1, 2020 Views: 1085 Forks: 0

original An abbreviated version of this protocol was published in eLife in Nov, 2014
Predicting evolution from the shape of genealogical trees
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Thank you for your interest in our paper. With more recent versions of fasttree, modification of the code should no longer be necessary. Instead, you can compile it with a flag indicating double precision:


http://www.microbesonline.org/fasttree/#BranchLen


Regarding the outgroup, you could use a strain from the early 1990ies like this one:


https://www.fludb.org/brc/fluStrainDetails.spg?strainName=A/Beijing/32/1992(H3N2)&decorator=influenza


 

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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. Neher, R and Shraiman, B(2020). Implementation of the inference algorithm. Bio-protocol Preprint. bio-protocol.org/prep350.
  2. Neher, R. A., Russell, C. A. and Shraiman, B. I.(2014). Predicting evolution from the shape of genealogical trees. eLife. DOI: 10.7554/eLife.03568

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