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BEAST tMRCA analysis on H5N1 2.3.4.4b strains from the US, including the strains from the March-April 2024 outbreak in dairy cattle

This analysis uses BEAST v1.10.4: https://beast.community.

File structure

  • mcc-gtrg-ucld-gmrf-colored.tre: a time-scaled maximum clade credibility HA gene tree generated from this analysis.
  • mcc-gtrg-ucld-gmrf-colored.pruned.tre: a paraphyletically subsampled HA phylogenetic tree used in Fig-S2.
  • GISAID-HA-genes.txt: lists the GISAID EPI identifiers for the seqeuences used in this analysis.
  • r8-100-gtrg-ucld-gmrf-noEPI.xml: a non-functional xml file generated by BEAUTI v1.10.4. This file has the GISAID sequence data removed and will not work.
  • additional XML files are provided to calculate the evolutionary rate for the cattle only clade (exponential and a GMRF Bayesian skyride coalescent model)

Step-by-step:

  1. Combine the GISAID sequences with the IRMA sequences from this analysis - genbank accessions pending.

  2. input into BEAUTI, parse the dates, and configure the analysis (GTR + gamma with estimated base frequencies; an uncorrelated relaxed lognormal clock; GMRF Bayesian Skyride with time aware smoothlng; uninformative priors; 100 million MCMC with sampling every 10,000)

  3. Analyses were run 5-8 times (50 million or 100 million, sampled to end with 10,000 states), and after inspection the logs and trees were combined (LogCombiner v1.10.4), and a single MCC was generated using TreeAnnotator v1.10.4.