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FreqType

piqtree.model.FreqType

Bases: Enum

Types of base frequencies.

F = 'F' class-attribute instance-attribute

FO = 'FO' class-attribute instance-attribute

FQ = 'FQ' class-attribute instance-attribute

description property

The description of the FreqType.

RETURNS DESCRIPTION
str

The description of the FreqType.

iqtree_str()

Source code in src/piqtree/model/_freq_type.py 
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def iqtree_str(self) -> str:
    return self.value

piqtree.model.CustomBaseFreq(frequencies)

For DNA models the order of the frequencies is:

A C G T

For AA models the order of the frequencies is:

A R N D C Q E G H I L K M F P S T W Y V
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val

IQ-TREE normalises the frequencies if they do not sum to one.

PARAMETER DESCRIPTION
frequencies

The fixed base frequencies.

TYPE: Sequence[float]

Source code in src/piqtree/model/_freq_type.py 
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def __init__(self, frequencies: Sequence[float]) -> None:
    """Create a custom base frequency specification.

    For DNA models the order of the frequencies is:

    A C G T

    For AA models the order of the frequencies is:

    | A   | R   | N   | D   | C   | Q  | E  | G  | H  | I  | L   | K   | M   | F   | P   | S   | T   | W   | Y   | V   |
    |-----|-----|-----|-----|-----|----|----|----|----|----|-----|-----|-----|-----|-----|-----|-----|-----|-----|-----|
    | Ala | Arg | Asn | Asp | Cys | Gln| Glu| Gly| His| Ile| Leu | Lys | Met | Phe | Pro | Ser | Thr | Trp | Tyr | Val |

    IQ-TREE normalises the frequencies if they do not sum to one.

    Parameters
    ----------
    frequencies : Sequence[float]
        The fixed base frequencies.

    """
    self.frequencies = frequencies

    if len(self.frequencies) not in (4, 20):
        msg = f"Expected either 4 frequencies for DNA model or 20 for AA model but got {len(self.frequencies)}"
        raise ValueError(msg)

Usage

For usage, see "Use different kinds of substitution models".