cocoatree.io.load_MSA

cocoatree.io.load_MSA(file_path, format='fasta', clean=True, verbose=False)

Read in a multiple sequence alignment (MSA)

Parameters

file_path : path to the alignment file

formatstring {“fasta”, “phylip”, …}, optional, default: “fasta”

format of the alignment file (e.g. ‘fasta’, ‘phylip’, etc.) All format supported by biopython’s Bio.AlignIO.read are accepted.

cleanboolean, default=True

whether to remove ambiguous amino acids (e.g. B, X etc.)

verboseboolean,

whether to print informations about the MSA

Returns

a dictionnary containing:

• sequences_id, list of sequence identifiers

• alignment: list of sequences as strings

Examples using cocoatree.io.load_MSA

Perform full SCA analysis on the S1A serine protease dataset

Perform full SCA analysis on the S1A serine protease dataset

Plot XCoR together with (phylogenetic) tree and metadata

Plot XCoR together with (phylogenetic) tree and metadata

Specifying metadata’s colors

Specifying metadata's colors

Plot a similarity heatmap of a XCoR along the phylogenetic tree

Plot a similarity heatmap of a XCoR along the phylogenetic tree