cocoatree.io.load_MSA¶
- cocoatree.io.load_MSA(file_path, format='fasta', clean=True, verbose=False)[source]¶
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¶
Plot sector together with (phylogenetic) tree and metadata
Plot sector together with (phylogenetic) tree and metadata
