Molecular epidemiology and phylogenetic analysis

Richard Neher
Biozentrum, University of Basel

slides at neherlab.org/202009_ECCVID_basics.html

Acknowledgments

Trevor Bedford and his lab -- terrific collaboration since 2014

especially James Hadfield, Emma Hodcroft, Ivan Aksamentov, Moira Zuber, and Tom Sibley

Data we analyze are contributed by scientists from all over the world

Data are shared and curated by GISAID

Sequences record the spread of pathogens

Mutations accumulate at a rate of $10^{-5}$ per site and day!

illustration by Trevor Bedford

Sequences and Alignment

  >SampleA

  ACGCYTCGCGTCGACTCGCTAC...

  >SampleB

  CYTCGCCTCGACTCGCTACGCA...

  >SampleC

  GCYTCGCGTCGACTCGCTACGC...

  >SampleC

  GCYTCGCGTCGAGCTACGCATG...

  >SampleA

  ACGCYTCGCGTCGACTCGCTAC---...

  >SampleB

  ---CYTCGCCTCGACTCGCTACGCA...

  >SampleC

  --GCYTCGCGTCGACTCGCTACGC-...

  >SampleC

  --GCYTCGCGTCGA---GCTACGCA...

Third party software: mafft, ClustalW, muscle...

Third party software: IQ-Tree, RAxML, fasttree...