09 Perl scripts to sequence manipulation

This is a collection of sequence manipulation scripts, including sequence cleaning and format conversion.
Download here!
How to run?

Download a script to directory where are your input file (fasta, nexus, phylip…). Execute the script by typing:

$perl ScriptName.pl InputFile OutputFile


Scripts list

  • SequCleaner.pl: clean sequences by removing non-alphabetical characters.
    Input: fasta sequence file.
    Output: cleaned fasta sequence file.
  • Nexus2Fasta.pl: convert sequence file in sequential nexus format to fasta format.
    Input: nexus sequence file.
    Output: fasta sequence file.
  • Phylip2Fasta.pl: convert sequence file in sequential phylip format to fasta format.
    Input: phylip sequence file.
    Output: fasta sequence file.
  • Fasta2Phylip.pl: convert sequence file in fasta format to sequential phylip format
    Input: fasta sequence file.
    Output: phylip sequence file.
  • Fasta2Nexus.pl: convert sequence file in fasta format to nexus format ***
    Input: fasta sequence file.
    Output: nexus sequence file.
    *** to execute type: $perl Fasta2Nexus.pl input.fasta > output.nex
  • Tbl2Fasta.pl: convert sequence file in table format to fasta format.
    Input: sequence table file (SeqName Sequence).
    Output: fasta sequence file.
  • GB2Fasta.pl: convert sequence file in GenBank format to fasta format.
    Input: sequence file in GenBank format.
    Output: fasta sequence file with sequence names created by combining GI number and GenBank accession number.
  • SwissProt2Fasta.pl: convert SwissProt output sequence file to fasta format.
    Input: SwissProt output sequence file.
    Output: fasta sequence file with sequence names created by combining swissprot id and accession number.
  • ReverseComplement.pl: calculate the reverse complement for DNA sequences.
    Input: DNA sequence fasta file.
    Output: reverse complemented sequence fasta file.
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