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Sorry to hear that. Preprint screening is a thankless task that unfortunately can misfire, but this sounds ridiculous. Not sure where you submitted, but you could try the q-bio.PE section on arxiv.org

Congratulations!!!

It'll hopefully be a while before we get there. But then I imagine we do the same as pango did for SC2 and use double letters.

Congratulations! Can't think of a better choice! 🎉

Congratulations!!

"little linkage within subgroups" means that mutations occur pretty independently of each other on different genetic backgrounds within the group. But mutations differentiating the larger subgroups tend to co-occur irrespective of their separation along the chromosome.

Analyzing these data as pangenome graphs was very helpful to disentangle contributions of homologous recombination and accessory genome evolution at different scales. I hope this will continue to help us to shed light on the dynamic world of bacteria and phages. [6/6] docs.pangraph.org

Introduction to Pangraph | Pangraph docsPangraph is currently under heavy development. Bugs and crashes are to be expected.docs.pangraph.org

This wide-spread homologous recombination seems to happen despite often substantial divergence >5% between genomes. But sometimes populations seem to fragment into groups with much less exchange – whether this is driven by geographic separation, ecological factors, or divergence is unclear. [5/6]

Within the syntenic core genome, linkage between SNPs decays rapidly with distance. LD approaches background levels after about 1000 bases. The background level itself is often set by population structure with little linkage within subgroups but genome wide coupling across subgroups. [4/6]

Using these cluster-wide pangenome graphs, we find a strongly conserved synteny of core phams. Accessory genome diversity is typically concentrated in well defined hotspots. [3/6]

Phages are known to recombine with each other and have flexible and fluid genomes. We analyzed diversity within the clusters of the Acinetobacteriophage Database by organizing their genomes into pangenome graphs based on homologous phams (protein families). [2/6]

Numbers came down quickly in early April, but the excess deaths accumulated through March corresponded roughly to the number of people that normally die in half a year.

In this case starting around 2013.

the coloring shows the cumulative count of amino acid substitutions from the root to the tip at a subset position that corresponds to prominent epitopes.