PHYLIP alignment (relaxed names) to UCSC nib converter

Convert a PHYLIP alignment (relaxed names) sequence file to UCSC nib.

Convert from Convert to Choose your sequence file

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

PHYLIP alignment (relaxed names) → UCSC nib

This output format holds exactly one sequence. Upload a file with a single record.
UCSC nib stores only the DNA letters A, C, G, T, and N. Gaps, ambiguity codes, RNA (U), and protein letters are rejected.
UCSC nib does not store record names, so the output has no identifier.

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.phylip-relaxed", "phylip-relaxed",
                      "output.nib", "nib")
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.

 3 39
seq1  ATGGCCATTG TAATGGGCCG CTGAAAGGGT GCCCGATAG
seq2  ATGGCCATTG TAATGGGCCG CTGAAAGGGT GCCCGA---
seq3  ATGTTCGCGA TTGTAATGGG CCGCTGAAAG GGTGCCCGA

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.

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