Convert ABI / AB1 trace to PHYLIP alignment (interleaved)

Provided by bugaco.com

Convert a ABI / AB1 trace sequence file to PHYLIP alignment (interleaved).

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

ABI / AB1 trace → PHYLIP alignment (interleaved)

  • The called sequence is extracted from the trace; chromatogram data and peak information are not included.
  • 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.

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

Sample input file: ABI / AB1 trace

ABI / AB1 trace is a binary format, so it cannot be shown as text. Download the sample file to try the converter.

Download sample (sample.ab1, 204.3 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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