Utilities#

Constants#

pyfamsa.MIQS: scoring_matrices.ScoringMatrix#: The MIQS scoring matrix proposed by Yamada & Tomii (2014), used by default in FAMSA for scoring alignments until FAMSA v2.3.0 (PyFAMSA v0.6.0).

pyfamsa.PFASUM31: scoring_matrices.ScoringMatrix#: The PFASUM31 scoring matrix proposed by Keul & Hess (2017).

pyfamsa.PFASUM43: scoring_matrices.ScoringMatrix#: The PFASUM43 scoring matrix proposed by Keul & Hess (2017) and used by default in FAMSA for scoring alignments since FAMSA v2.3.0 (PyFAMSA v0.6.0).

pyfamsa.PFASUM60: scoring_matrices.ScoringMatrix#: The PFASUM60 scoring matrix proposed by Keul & Hess (2017).

pyfamsa.FAMSA_ALPHABET: str#: The alphabet used by FAMSA to encode input sequences.

Functions#

pyfamsa.famsa_info()#

Get information about the embedded FAMSA version.

This function returns an anonymous named tuple with attributes version, version_info, date and authors that can be used to get the build information from FAMSA.

Example

>>> info = famsa_info()
>>> info.version
'2.5.2'
>>> info.date
datetime.date(2026, 3, 23)