Fasta to Clustal Sequence Converter

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Convert file from: to
Alphabet: None DNA RNA Protein Nucleotide

Input format: fasta This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.

Output format: clustal The alignment format of Clustal X and Clustal W.

How to convert from fasta to clustal ?

You can also convert between these formats by using command line tools.
  • On Windows install WSL, on Mac or Linux start terminal
  • Install BioPython
  • Run following script:
    from Bio import SeqIO
    records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.fasta", "fasta")
    count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.clustal", "clustal")
    print("Converted %i records" % count)
  • Or you can use this site as online fasta to clustal converter by selecting your formats & file.

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