specify order of output of -C option in help message

sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file

http://sanger-pathogens.github.io/snp-sites/

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specify order of output of -C option in help message #88

Open amilesj opened 4 years ago

amilesj commented 4 years ago

Thanks for the new -C function for counting constant sites...super useful! Can I recommend explicitly stating that the output of -C is in A,C,G,T order in the help message? Some users might not know that alphabetical order is convention.

well-123-hub commented 4 years ago

Hi I have 101 bacteria genomes assembled in fna format. Can I use snp-site to identify snps into vcf format? Can u help with the appropriate command keys for this?

flass commented 4 years ago

this is relevant as this can be used to specify the paprameters of the ascertainment bias correction in the Stamatakis model of RAxML and RAxML-NG (see https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model), which also uses the A,C,G,T character order for DNA models (syntax being --model BASEMODEL+ASC_STAM{wA/wC/wG/wT}).