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Output invariant sites and nucleotide frequencies #62
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I second this suggestion. Either add a OR Always output this to |
Grand, give me a toy example and I'll sort it out
…On 27 September 2017 at 08:53, Torsten Seemann ***@***.***> wrote:
I second this suggestion.
Either add a -s (stats?) option to report all sorts of columnar
statistics, characters used etc.
OR
Always output this to stderr as part of the logs.
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From your example in the README:
-s (or stderr) would produce: Input stats: Output stats: Thinking about this more, I obviously came up with a couple other useful stats. seqtk comp can produce similar stats, but having them in one tool with the speed of SNP-sites would be great. |
But output in a machine readable format so we can parse or JSON-ate. |
Hello. I was curious if this was ever implemented? |
In general, phylogenetic programs use invariant sites for likelihood calculations. However, a number of programs, such as RAxML and BEAST, can perform ascertainment bias corrections given the number of invariant sites and the frequencies of nucleotides in the alignment. If SNP-sites output these values, they could be used as direct inputs for RAxML, for example.
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