cocoatree.io.load_MSA

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

Read in a multiple sequence alignment (MSA)

Arguments

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

Plot sector together with (phylogenetic) tree and metadata

Plot sector together with (phylogenetic) tree and metadata