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While checking our molecular clock assumptions, I thought I'd grab a few of the B.1.1.529 genomes to see where they fall (open red circles). Red line assumes 8e-4 subs/nt/yr. Black lines show 0.1% and 99.9% of Poisson distribution.

Our first filogeneti.ca/CoVizu update with B.1.1.529. As expected, number of mutations is well over molecular clock prediction (~13 diffs). Relatively low numbers of identical genomes implies large number of unsampled infections. We update every two days from GISAID.

Laura's 1st first-author paper as my PhD student is finally out. Her original MS got scooped, so we spent an extra year creating a new method to analyze overlapping genes in viruses. Congrats Laura! Next one will be easier, I swear 😄 #PLOSPathogens dx.plos.org/10.1371/journa…

New feature addition to filogeneti.ca/CoVizu: You can now view mutations associated with any lineage under the "Mutations" tab, with their frequencies and phenotypic effects (thanks to Paul Gordon's Pokay repo). Thanks to Bonnie, An, Abayomi and Gopi for making this happen.

I'm very grateful to CIHR and the Genomics review panel for funding my Project Grant! This will sustain ongoing development of our real-time #SARSCoV2 tracking system (filogeneti.ca/CoVizu), as well as new #bioinformatics methods in virus evolution and epidemiology.

New feature at filogeneti.ca/CoVizu: You can now use a slider to vary the number of lineages displayed in the tree, based on when they were last sampled. Since many lineages are no longer circulating, this can greatly reduce the size of the tree!

I have a job opening at #WesternU for a part-time programmer (15-24h/wk, $30/h) to work with us on building open-source virus evol/epi apps. Needs exp. with ≥1 of {Python, R, JS}, collab. coding w/git, remote work OK! Please see recruit.uwo.ca, Job ID 28400

fwiw this is an interactive streamgraph that I implemented using #rstudio's r2d3 interface to pass data from R to some customized D3.js open source: github.com/CoVaRR-NET/duo…

Abstract submission deadline for the 30th International Dynamics & Evolution of Human Viruses meeting in Germany has been extended to Jan 15: dynamicsevolution.org/event/1/