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rasmushenningsson / DISSEQT.jl

DISSEQT – DIStribution based modeling of SEQuence Space Time dynamics
MIT License
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Is this tool can be use with multi-sequence alignment？ #2

Open virologist opened 3 years ago

virologist commented 3 years ago

Hi, @rasmushenningsson

I am wondering to know can DISSEQT be used with virus multiple sequences alignment (MSA) collected from different dates? If I was understood correctly, DISSEQT used NGS data collected from single or multiple samples to detect the fitness landscapes of the virus population. Suppose I want to detect the viral fitness landscapes over a period of time, it that possible to do with MSA rather than NGS data?

Best wishes, Yang

rasmushenningsson commented 3 years ago

Hi!

As long as you have BAM files it should work fine. DISSEQT doesn't handle indels, but within a "mutant swarm" or "quasi-species" it is often reasonable to only expect substitutions. In our case, we mostly used DISSEQT for Coxsackievirus B3, where this is true.

Note that you also need empirical fitness measurements for each sample to produce the fitness landscape.

I would recommend using all samples to create a single fitness landscape (assuming that the environment doesn't change), then you can see whether samples move to high fitness areas as time passes.

virologist commented 3 years ago

Hi, @rasmushenningsson

Thanks for your quick reply. Based on the description of these 2 links 1 and 2, it may not be a good idea to convert the fasta to BAM.

Thanks anyway Yang