UCSC nib to Clustal alignment converter

Convert a UCSC nib sequence file to Clustal alignment.

Convert from Convert to Choose your sequence file

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

UCSC nib → Clustal alignment

Clustal keeps only the first 30 characters of each record ID (and replaces spaces 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.nib", "nib",
                      "output.clustal", "clustal")
print("Converted %i records" % count)

Sample input file: UCSC nib

UCSC nib is a binary format, so it cannot be shown as text. Download the sample file to try the converter.

Download sample (sample.nib, 38 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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