Convert FASTA to PHYLIP alignment (interleaved)

Provided by bugaco.com

Convert a FASTA sequence file to PHYLIP alignment (interleaved).

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

FASTA → PHYLIP alignment (interleaved)

  • PHYLIP keeps only the first 10 characters of each record ID (and replaces : and ; with |). IDs that become identical are rejected.
  • The selected output is an alignment format. Every sequence must be the same length and already aligned. This does not create an alignment.
  • The output keeps only each record's ID, so description text (such as the words after the ID on a FASTA header line) is not kept.

Writing an aligned FASTA file as interleaved PHYLIP

Yes, this page converts FASTA to PHYLIP alignment (interleaved), provided the sequences are already aligned to the same length; the converter does not align them. IDs longer than 10 characters are cut, and any description after the ID is dropped. No sequence-type question is asked for this pair.

What carries over into the PHYLIP file

Data in your file In the output Details
Aligned sequence rows Kept Written as the rows of one interleaved alignment; in the sample, every letter comes through unchanged.
Record IDs Changed if needed Shortened if longer than 10 characters; a colon or semicolon becomes a vertical bar.
Header description text Lost Words after the ID on a header line are not kept.

Rules the converter applies before writing

  • Every sequence must have the same length; a record that differs is refused, and the message gives both lengths. The converter does not align or pad anything.
  • A record with no sequence letters is refused.
  • A period in a sequence is refused. The message asks you to replace each . with -, the gap symbol, and convert again.
  • Two IDs that become identical after shortening to 10 characters are refused. The message asks you to rename the records so that their first 10 characters differ.

The sample on this page converts

The sample file holds three records of 39 letters each, named seq1 to seq3. It converts to a three-row interleaved alignment whose first line reads 3 39; the IDs seq1 to seq3 stay as they are, the letters come through unchanged, and the words after each ID are gone.

Longer names, sequential layout, and the way back

FASTA to PHYLIP alignment (relaxed names) does not shorten IDs to 10 characters; instead, every ID must be present, unique, and free of spaces or other whitespace. It has the same equal-length, no-empty-record, and no-period rules and still drops descriptions. FASTA to PHYLIP alignment (sequential) writes the sequential layout with the same 10-character rule as this page. Both convert the sample as well.

The reverse route, PHYLIP alignment (interleaved) to FASTA, is available and has no loss notices, but it cannot restore characters cut from the IDs or descriptions dropped here.

If the file is refused for another reason

If the upload cannot be read at all, the page says only that it could not be read as FASTA and asks you to check that it is a valid FASTA file; no cause is given. Uploads are limited to 50 MB.

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.fasta", "fasta",
                      "output.phylip", "phylip")
print("Converted %i records" % count)

Sample input file: FASTA

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

Download sample (sample.fasta, 210 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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