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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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Mutation Rate Table output #81

Open LisaCarraro opened 2 years ago

LisaCarraro commented 2 years ago

Hallo, if i find 36/3348654 (value obtained comparing 2 isolates) in Mutation Rate Table, 3348654 is the total number of nucleotides aligned in these 2 isolates?

Thank you very much Best Lisa

fasnicar commented 2 years ago

Hi Lisa, The values reflect the different positions over the total number of positions that can be compared. This means that gaps, for instance, won't be considered in the mutation rates estimation. The mutation rates table is computed before any trimming and/or subsampling, if any, so will be computed on the very first multiple-sequence alignments.

I hope this helps.

Thanks, Francesco

LisaCarraro commented 2 years ago

Thank you very much!! Lisa