FASTA#

FASTA is a simple text-based format for sequence data, widely used in bioinformatics. Each sequence has a header line starting with > followed by one or more lines of sequence characters.

See also

FASTA format — Wikipedia

Classes and extensions#

Classes: MSA (default format)

File extensions: .fasta, .fa, .fas

Structure#

>taxon1
ACGTACGT
>taxon2
TGCAACGT
>taxon3
AAAAACGT

Examples#

from phylozoo import MSA
sequences = {
    "taxon1": "ACGTACGT",
    "taxon2": "TGCAACGT",
    "taxon3": "AAAAACGT"
}
msa = MSA(sequences)
msa.save("alignment.fasta")
msa2 = MSA.load("alignment.fasta")
fasta_str = msa.to_string(format="fasta", line_length=60)

See also#