Post date: May 26, 2020 2:0:44 PM
Email exchanges with Ozan!
Hi Rozenn,
Thanks again for the presentation. It was a lot of fun & it was very clearly presented.
I don't think you need to read those papers below. I did not!.. It is just they may be inspirational.
For instance, it is nice to see different ways of connecting networks from genotype data or how genetic distance aligns with spatial distribution (e.g. when phylogeny is placed next to spatial distribution it is easy to see what is going on). Other than that, as we talked, clones you have may be soooo similar with few informative sites, then this alignment/phylogeny based analysis may fall short and be a waste of time. And since alignment is also distance based, it should not be that different than what you did, but it can gather some more info from data, such as mutations in all sites can be used with this method and mutations like insertion/deletion (i.e. indels) can connect more similar individuals into clades more powerfully (I am not perfectly sure!). Also inferring phases of alleles when concatenating alleles requires some tricky software applications. But that should be solvable.
Fig2&3 https://static-curis.ku.dk/portal/files/201003963/file.pdf
Fig4 https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007807
Fig1B https://www.biorxiv.org/content/10.1101/622019v2.full.pdf
Fig1AvsC https://elifesciences.org/articles/12081
Fig5 etc https://europepmc.org/article/PMC/5988311
Understanding IBD
http://www.mun.ca/biology/scarr/Identity_by_descent.htm
Generate neighbor joining trees from SNVs
generate neighbor-joining trees using Phylip: https://elifesciences.org/articles/12081