xavierdidelot
commented
5 years ago Hi Yu,
No worries, I'm very happy to answer questions about TransPhylo and/or BactDating.
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yes this is fine.
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indeed, these two parameters determine the generation distribution which depends on the pathogen you're studying. For Klebsiella a recent paper (van Dorp et al, MGen 2019) used w.shape=1 and w.scale=0.5 so you could use this at least as a starting point.
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unfortunately at the moment TransPhylo is unable to use more than one isolate per patient.I would recommend selecting one isolate per patient at random.
Best wishes, Xavier
Hi, It's me again, thanks for this lovely program. I've got a few questions, if you please
1) I'm wondering if it is correct to use the output of BactDating as the input for TransPhylo, by using "write.tree(result$tree,'tree.nwk')", where "result" is the output of BactDating.
2) In the example, w.shape=10 and w.scale=0.1 were used, however in your paper, of the TB case, w.shape=1.3 and w.scale=0.3 were used instead. Such two sets of parameters varies largely, so I'm wondering how I can determine the generation time parameter for my own dataset, a group of very closely related (pairwise SNP < 20) Klebsiella pneumoniae strains? which example should be used as the start point?
3) In an outbreak analysis, multiple isolates were sampled from the same patient at different time points, can I use them all in the transphylo analysis? or I should just leave one for each patient on the tree?
sorry for asking these questions and many thanks to you.
Yu