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gstecher / CloneFinderAPI

API for the Clone Finder application
MIT License
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Cancer Subclonal Tree #1

Open zorrodong opened 6 years ago

zorrodong commented 6 years ago

Hi,

Thanks for the powerful tool to infer cancer subclones. I have two questions for this tool: 1, you recommended to use at leat 4 samples to perform the analysis. However, I only have three tumor samples from one patient, I wonder whether I can still use this tool, and, what if I have only one sample ?

2, for the result file: XXX.meg, can I directly use MEGA software to construct the phylogenetic tree through this file ? And which tree method should use? NJ, MP, ML or others ?

And If I want to use the normal sample as outgroup in the tree, so can I just add a sequence with all "A" ?

Looking forward to your reply!

Thanks very much!

Best,

Zorro 2018.06.14

SayakaMiura commented 4 years ago

I am sorry for very late reply.

  1. You can use CloneFinder for a dataset with three tumor samples, but the result may not be so accurate. CloneFinder will not run for dataset with only one or two samples.
  2. Yes, you can use MEGA software to reconstruct the tree. I recommend MP.
  3. Yes, the sequence of a normal sample is all "A."