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donkeyshot / phybreak

Outbreak reconstruction with sequence data
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collection dates unclear #5

Open tigerxu opened 6 years ago

tigerxu commented 6 years ago

Hi Don,

In my case, the collection dates of certain strains are unclear, e.g. like these 2009-11-XX or 2009-XX-XX. Is it possible to apply phybreak for such analysis?

Thanks!

Zhuofei

donkeyshot commented 6 years ago

Hi Zhuofei It's not possible to explicitly include uncertainty about collection dates.  If for all samples you only have months you can enter collection times as nth month. If precision is different for different samples, you will have to choose specific dates for some samples. I could imagine implementing collection intervals which phybreak could interpret as a uniform prior for the collection date. Would that be useful for you? Best wishesDon -------- Oorspronkelijk bericht --------Van: tigerxu notifications@github.com Datum: 22-10-18 08:52 (GMT+01:00) Aan: donkeyshot/phybreak phybreak@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Onderwerp: [donkeyshot/phybreak] collection dates unclear (#5) Hi Don, In my case, the collection dates of certain strains are unclear, e.g. like these 2009-11-XX or 2009-XX-XX. Is it possible to apply phybreak for such analysis? Thanks! Zhuofei

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tigerxu commented 6 years ago

Hi Don,

Many thanks for your prompt reply! I understand. I will try to use nth month for sampling dates. Sampling during an outbreak often has a clear start and end date. It's useful to add collection intervals.

In my collected data (~300 viral genomes and metadata during 27 years, I found some highly genetically similar strains are clustered into a single group which is likely to belong to a long-term epidemic over 10 years. In the FMDV case using phybreak, all isolates are collected within several months. So I'm wondering if it is suitable for using phybreak to analyze these data with a long time range?

Best wishes, Zhuofei