Convert mmCIF structure (declared sequence) to PHYLIP alignment (interleaved)

Provided by bugaco.com

Convert a mmCIF structure (declared sequence) sequence file to PHYLIP alignment (interleaved).

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

mmCIF structure (declared sequence) → PHYLIP alignment (interleaved)

  • This reads the full sequence declared by the structure record, which may differ from observed coordinates.
  • 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.

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.cif-seqres", "cif-seqres",
                      "output.phylip", "phylip")
print("Converted %i records" % count)

Sample input file: mmCIF structure (declared sequence)

Copy this example into a file, or download it, to try a mmCIF structure (declared sequence) conversion.

Download sample (sample.cif, 407 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.

Choose another conversion