sequence assembly
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DNA contig assembly

Clone Library Dereplicator

Dereplicate your clone libraries in a matter of moments


dna assembly software




Tool description


When building clone libraries it is often the case that many of the sequenced clones are 100% identical. Therefore, before further DNA sequence analysis, it is necessary to find duplicate DNA sequences and remove them. Our DNA sequence dereplication tool sorts all unique DNA sequences (FASTA) belonging to your clone libraries, by moving/coping them into the specified folder.


Clone Library Dereplicator simplifies the dereplication of all type sequence libraries (16S rRNA, 18S rRNA, 23S rRNA, 28S rRNA, functional and structural proteins) and prepares the raw sequences for subsequent analyses or contig assembly.



The tool is located under the 'Tools->Clone library dereplicatior' menu in DNA Sequence Assembler.




How to use it

  1. Choose the input folder - the folder that contains the FASTA sequences that need to be de-replicated.
  2. Choose output folder - the folder where the unique files will be copied/moved. For your commodity, DNA Sequence Dereplicator will create an output folder for you so you can skip this step.
  3. Choose file operation type. This will instruct the program whether to copy or move the unique files from the input folder to the output folder.
  4. Choose comparison type:
    • 'Text match' will make a direct comparison between the sequences. This is very fast but it can't tell you how many differences have been found between sequences.
    • 'Global alignment' will compare the sequences by using a global alignment algorithm. Slow.
  5. Press the 'Dereplicate' button.





Clone Library Dereplicator is freeware. Starting with August 2008, Clone Library Dereplicator was integrated into the DNA Sequence Assembler package. It is still freeware.


Download DNA sequence alignment software



Important news


We have a new tool that can dereplicate large (GB) sets of sequences. Please see the new Sequence Dereplicator.



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