Instructions for Sequence Manipulator

This is a collection of sequence manipulation scripts, including sequence cleaning and format conversion.

How to run

  1. Download a program below to your local computer, and set it as executable by typing the following command in your working directory:

    chmod +x [ProgramName]

  2. Create a subdirectory in your working directory to hold input files and output files. In the subdirectory, type following command:

    perl ../[ProgramName] InputFile OutputFile

Program list

  1. SequCleaner.pl: clean sequences by removing non-alphabetical characters.

    Input: fasta sequence file.

    Output: cleaned fasta sequence file.

    Download

  2. Nexus2Fasta.pl: convert sequence file in sequential nexus format to fasta format.

    Input: nexus sequence file.

    Output: fasta sequence file.

    Download

  3. Phylip2Fasta.pl: convert sequence file in sequential phylip format to fasta format.

    Input: phylip sequence file.

    Output: fasta sequence file.

    Download

  4. Fasta2Phylip.pl: convert sequence file in fasta format to sequential phylip format

    Input: fasta sequence file.

    Output: phylip sequence file.

    Download

  5. Tbl2Fasta.pl: convert sequence file in table format to fasta format.

    Input: sequence table file (SeqName Sequence).

    Output: fasta sequence file.

    Download

  6. 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.

    Download

  7. 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.

    Download

  8. ReverseComplement.pl: calculate the reverse complement for DNA sequences.

    Input: DNA sequence fasta file.

    Output: reverse complemented sequence fasta file.

    Download