J X and Z residues seen in amino acid ancestral reconstruction states file

Aderounmu Adedeji

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Oct 28, 2020, 12:29:27 AM10/28/20

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Hello raxml team,

I am writing because i notice a few non-amino acid residues, specifically J X and Z, in the AncestralStates file when I use raxml-ng to perform ancestral reconstruction. Is there a reason this happens and is there a fix for it?

Thank you

Alexey Kozlov

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Oct 28, 2020, 6:41:59 AM10/28/20

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Hi Aderounmu,

those three symbols encode ambiguous amino acid states, please see:

https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes

Best,
Alexey

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Aderounmu Adedeji

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Oct 28, 2020, 5:12:04 PM10/28/20

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Alright. Thank you.

Adedeji

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