Convert MAF alignment to PHYLIP alignment (sequential)

Provided by bugaco.com

Convert a MAF alignment sequence file to PHYLIP alignment (sequential).

Maximum file size: 50 MB. The file is checked before conversion.

MAF alignment → PHYLIP alignment (sequential)

  • PHYLIP keeps only the first 10 characters of each record ID (and replaces : and ; with |). IDs that become identical are rejected.
  • Only the aligned sequence rows are converted; alignment annotations such as scores and consensus lines are not kept. A file with several alignments can be converted only to sequence formats such as FASTA.
  • The selected output is an alignment format. Every sequence must be the same length and already aligned. This does not create an alignment.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The notes under the Convert file button list the important limits for this pair.

The converter writes one alignment per PHYLIP alignment (sequential) file, so upload one alignment at a time. A file with several alignments (for example several MAF blocks or Stockholm sections) is refused rather than merged into one.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

count = SeqIO.convert("input.maf", "maf",
                      "output.phylip-sequential", "phylip-sequential")
print("Converted %i records" % count)

Sample input file: MAF alignment

Copy this example into a file, or download it, to try a MAF alignment conversion.

Download sample (sample.maf, 438 bytes)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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