The Embedded Alphabet (TEA) This repository contains the code accompanying our pre print (link coming soon). Installation Sequence Conversion with TEA The tea convert command takes protein sequences from a FASTA file and generates new tea FASTA. It supports confidence based sequence output where low confidence positions are displayed in lowercase, and has options for saving logits and entropy. If save avg entropy is set, the FASTA identifiers will contain the average entropy of the sequence in the format H= . Using the huggingface model Using tea sequences with MMseqs2 The matcha.out substitution matrix is included with the tea package. You can get its path programmatically: Then use it with MMseqs2:
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