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pyMSA has only two available substitution matrices: *PAM250* and *Blosum62*.
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Other substitution matrices can be used by reading a matrix [file](ftp://ftp.ncbi.nih.gov/blast/matrices/) with `read_matrix_from_file()` (from `pymsa.util.substitution_matrix` module).
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`FileMatrix` implements this method by default:
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Other substitution matrices can be used by reading a matrix [file](ftp://ftp.ncbi.nih.gov/blast/matrices/) with `read_matrix_from_file()` (from the `pymsa.util.substitution_matrix` module). `FileMatrix` implements this method by default:
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```python
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from pymsa.core.substitution_matrix importPAM250, Blosum62, FileMatrix
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