Convert a PHYLIP alignment (relaxed names) sequence file to Stockholm 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 Stockholm 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 pair needs no molecule type argument.
from Bio import SeqIO
count = SeqIO.convert("input.phylip-relaxed", "phylip-relaxed",
"output.stockholm", "stockholm")
print("Converted %i records" % count)Sample input file: PHYLIP alignment (relaxed names)
Copy this example into a file, or download it, to try a PHYLIP alignment (relaxed names) conversion.
Download sample (sample.phy, 153 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.