Convert EMBOSS pairwise alignment to NEXUS alignment

Provided by bugaco.com

Convert a EMBOSS pairwise alignment sequence file to NEXUS alignment.

This output needs a sequence type. The selected input format does not record it, so the converter will use your choice.

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

EMBOSS pairwise alignment → NEXUS alignment

  • 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 NEXUS alignment 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 output needs a sequence type, so replace the example molecule type with DNA, RNA, or protein to match your file.

from Bio import SeqIO

count = SeqIO.convert("input.emboss", "emboss",
                      "output.nexus", "nexus",
                      molecule_type="DNA")
print("Converted %i records" % count)

Sample input file: EMBOSS pairwise alignment

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

Download sample (sample.txt, 1.2 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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