famsa will replace the amino acid U with X

refresh-bio / FAMSA

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

GNU General Public License v3.0

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famsa will replace the amino acid U with X #27

Closed LTEnjoy closed 2 years ago

LTEnjoy commented 2 years ago

Hello! When I used famsa to alignment sequences, it would automatically replace all the amino acid U with X and keep others the same. Could you solve this problem?

agudys commented 2 years ago

Hello!

Thank you for reporting this issue. Selenocysteine is not among standard 20 amino acids, thus it is treated by FAMSA as an unknown symbol and replaced with X in the final alignment. I am marking support of extra amino-acids as a TODO feature.

Adam

agudys commented 2 years ago

The issue has been fixed in the latest sources. Please verify if it works as expected.