This protocol is provided by the author(s) of the original paper via Bio-protocol's "Request a Protocol" feature.
Original Research Paper Predicting evolution from the shape of genealogical trees
DOI: 10.7554/eLife.03568
eLIFE , Nov 11, 2014
Related protocols in the same article
Implementation of the inference algorithm
Last updated date: Jul 1, 2020 View: 160
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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


 

How to cite: Readers should cite both the Bio-protocol article and the original research article where this protocol was used:
1. Neher, R. and Shraiman, B. (2020). Implementation of the inference algorithm. Bio-protocol. bio-protocol.org/prep350.
2. Neher, R., Russell, C. and Shraiman, B.(2014). Predicting evolution from the shape of genealogical trees. eLIFE . DOI: 10.7554/eLife.03568
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