Module clustal

Returns a path to ClustalW executable.

This function attempts to find clustalw2 excutable in following locations:

1) Maestro bin directory based on MAESTRO_EXEC env var. 2) Maestro bin directory based on $SCHRODINGER/maestro-v*/bin/* path. 3) User-defined location (CLUSTALW2 env var).

Returns: str

path to ClustalW executable file, or None if the executable could not be located.

Writes alignment to a file, runs ClustalW alignment program and reads the results back.

This function can use one of three available alignment modes:

• regular multiple sequence alignment,
• profile-profile alignment where two alignments are aligned to each other, but both alignments remain unchanged,
• profile-sequence alignment where several sequences are iteratively aligned to existing alignment.

Parameters:

• aln (ProteinAlignment) - Input sequence alignment.
• second_aln (ProteinAlignment) - Second alignment for profile-profile and profile-sequence alignment.
• profile_mode (str) - Determines profile alignment mode. Can be "profile" for profile-profile alignment, or "sequences" for profile-sequence alignment.
• matrix (str or None) - substitution matrix family ("BLOSUM", "PAM", "GONNET", "ID") If None, default matrix (GONNET) is used.
• gapopen (float or None) - Gap opening penalty. If None, default value is used.
• gapext (float or None) - Gap extension penalty. If None, default value is used.
• quicktree (bool) - Use fast algorithm for building guide tree. Default value is False.

Returns: tuple of (ProteinAlignment, str) or None

Output alignment and tree string. The sequences are output in the same order as input. Sequence attributes are preserved. The tree is in Newick format. This function returns None if ClustalW executable cannot be found.