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xavierdidelot / ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
GNU General Public License v3.0
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different outputs with different parameters, how to choose the rihgt one? #109

Closed cheerupgirls closed 4 years ago

cheerupgirls commented 4 years ago

Hi Xavier, what does it mean that the output is being too conservative in issue #30? Any method to identify it? Is it normal that the outputs vary with differernt parameter (such as -embranch_dispersion or model) or subsets of my data? I'm not sure weather this result is due to my sample size is small (37, but some of them are very similar ) or something else. Any advice is welcome, thank you.

Best wishes, Ajiao

xavierdidelot commented 4 years ago

Hi Ajiao,

In issue #30 by "too conservative" I meant that ClonalFrameML detects a lot less recombination than you would expect. Yes you would expect to get different outputs when you use different parameter values, especially on a small dataset. For a small dataset it is probably best to stick with the default (ie not per-branch) model.

Best wishes, Xavier