biotite
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Support for A2M/A3M files
Reading/writing MSAs from/to A3M files might be a useful addition to Biotite. A2M/A3M files are quite commonly accepted as input/produced by alignment programs or protein structure prediction pipelines (e.g. MMseqs2, RoseTTAFold and AlphaFold3). The format itself offers additional notation for inserted amino acids.
I did not know RoseTTAFold also uses A3M format. I already have some functionality regarding this for private usage, so I will sanitize the code and prepare a PR for this in the upcoming weeks