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We have a pretty weak dependency on `polyclonal` - we could remove this by simply adding our own alphabets, and mutation parser. Although, I wonder if these could be part of binarymap :thinking: @jblo…
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I am analyzing 8 tumors and based on CCF and unsupervised heirchal clustering I'm expecting one of my tumors to have been seeded by two separate tumors. How does PhyloWGS handle this? Would this show …
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Hi，
I am trying to get the JSON results, and got an error as follows:
Traceback (most recent call last):
File "/data1/software/phloWGS/phylowgs/write_results.py", line 41, in
main()
…
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Hello!
I was just wondering if this software would be useful to determine full haplotypes or quasispecies in "multiple" CRISPR edited polyclonal mixtures (for example 2 sgRNA's cutting close to each …
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Currently in [S_convalescent_plasma_escape.txt](https://github.com/nodrogluap/pokay/blob/master/data/literature/NC_045512/S_convalescent_plasma_escape.txt), we have:
```
# Mutant found after in pa…
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Hi, I recently started to use phylowgs but come across with following error when running with my samples. (c.f. running with example data had no issues, I double checked ssm files)
[2019-03-01 17:0…
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### Select the target metadata schema name (can be multiple), or choose 'Other' if not listed.
Other
### If 'Other' is selected, please enter the schema name below.
AVR
### Describe the change req…
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Hi, thanks for the wonderful tool you developed!
Can you help me deal with a issue? while I was using your example data from aml1$variants and the code you provided in the manual, everything was fine…
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Hi
I have 50 patients who have responded to chemotherapy from which 17 samples are pre-treatment biopsies and 33 patients post-treatment resections. The pre and post samples are not matched. I want…
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Only a single outbreak group is listed in the Listeria dataset (1408MLGX6-3WGS), but I haven't been able to create a phylogenetic tree that captures these samples in a single clade.
I also noticed …