PHRED PHD to PHYLIP alignment (sequential) converter

Convert a PHRED PHD sequence file to PHYLIP alignment (sequential).

Convert from Convert to Choose your sequence file

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

PHRED PHD → PHYLIP alignment (sequential)

PHYLIP keeps only the first 10 characters of each record ID (and replaces : and ; with |). IDs that become identical are rejected.
The output keeps sequence letters but removes per-base quality scores.
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.

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.

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.phd", "phd",
                      "output.phylip-sequential", "phylip-sequential")
print("Converted %i records" % count)

Sample input file: PHRED PHD

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

BEGIN_SEQUENCE read1 example read 1
BEGIN_COMMENT
END_COMMENT
BEGIN_DNA
G 40
A 40
T 40
T 40
T 40
G 40
G 40
G 40
G 40
T 39
T 39
C 39
A 39
A 39
A 39
G 39
C 39
A 39
G 38
T 38
A 38
T 38
C 38
G 38
A 38
T 38
C 37
A 37
A 37
A 37
T 37
A 37
G 37
T 37
A 37
A 36
A 36
T 36
C 36
C 36
A 36
T 36
T 36
T 35
G 35
T 35
T 35
C 35
A 35
A 35
C 35
T 35
C 34
A 34
C 34
A 34
G 34
T 34
T 34
T 34
END_DNA
END_SEQUENCE
BEGIN_SEQUENCE read2 example read 2
BEGIN_COMMENT
END_COMMENT
BEGIN_DNA
G 40
A 40
T 40
T 40
T 40
G 40
G 40
G 39
G 39
T 39
T 39
C 39
A 39
A 39
A 38
G 38
C 38
A 38
G 38
T 38
A 38
T 37
C 37
G 37
A 37
T 37
C 37
A 37
A 36
A 36
T 36
A 36
G 36
T 36
A 36
A 35
A 35
T 35
C 35
C 35
A 35
T 35
T 34
T 34
G 34
T 34
T 34
C 34
END_DNA
END_SEQUENCE
BEGIN_SEQUENCE read3 example read 3
BEGIN_COMMENT
END_COMMENT
BEGIN_DNA
T 40
T 40
G 40
G 40
G 40
G 40
T 40
T 40
C 39
A 39
A 39
A 39
G 39
C 39
A 39
G 38
T 38
A 38
T 38
C 38
G 38
A 38
T 37
C 37
A 37
A 37
A 37
T 37
A 37
G 36
T 36
A 36
A 36
A 36
T 36
C 36
C 35
A 35
T 35
T 35
T 35
G 35
T 35
T 34
C 34
A 34
A 34
C 34
T 34
C 34
END_DNA
END_SEQUENCE

Download sample (sample.phd, 1.0 KB)

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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