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Even Better Free Molecular Biology Software: Serial Cloner

Even Better Free Molecular Biology Software: Serial Cloner

In 2007, I wrote a couple of articles on the best free software for molecular biologists on Mac and PC. One of the highlights of those lists was a fantastic cross-platform for in silico DNA cloning, sequence analysis and visualization, called Serial Cloner (move over VectorNTI!).

sc-screen-smallThe creator of Serial Cloner, Franck Perez, contacted me recently to tell me that he had just released an excellent new version of the  software and asked if I would relay this to our readers. Well, as a big fan of Serial Cloner I am only too happy to oblige.

If you do molecular biology and you haven’t tried our Serial Cloner, I’d urge you to give it a go. It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.

Among the many improvements Franck has made in this new version are:

  • Automatic scanning for features in imported sequences
  • Importing VectorNTI, Genbank, EMBL, ApE sequences with features
  • Generation of MultiFasta formated sequence for Clustal submission
  • Recovery of unsaved sequence in case of unexpected quit
  • Impoved Import of NCBI/EMBL sequences (Web Access)
  • Alignments via NCBI BLAST2seq

Check it out at http://serialbasics.free.fr/Serial_Cloner.html


  1. Niraj Joshi on October 9, 2019 at 5:28 pm

    Hello All,

    It does not work on a newer platform of Mac OS10.5. Can anyone help me?

  2. sameerbau on February 8, 2011 at 7:41 pm


    I used the serial cloner’s latest version and found it really useful.even though our lab does not have frequent cloning work,i find the double stranded viewer..really handy while designing primers..

    I was thinking if you could recommend some good pathway designer
    software.You know it really takes a lot of time for somebody not well
    versed with GIMP/photoshop/illustrator/corel to make their pathway
    images or explain concepts using pictures for some publication or for
    teaching to students or for condensing matter from various papers..

    And also is there a place to download stock images for making such illustrations?

    Kindly help…or maybe write an article on the same!(don’t forget to care about windows users too)


  3. Franck Perez on May 27, 2010 at 7:25 pm

    Dear all,

    Just a quick message to announce you that I released version 2.1 of Serial Cloner.
    It is a much improved version so I strongly advice users to update. A non-users to give a try !
    It is still, and will always be, a freeware (although donations are welcome).

    Main improvements (among tens of changes) :

    – [NEW] Define user’s Feature Collection (DNA, Peptide)
    – [NEW] Import/Export Features collections
    – [NEW] Export Sequences in GenBank format (with Features)
    – [NEW] Directly send BLAST request to NCBI.
    – [NEW] Two Companion Software to import MacVector files and to Reset Serial Cloner
    – [ADDED] Search for a peptide sequence using the Find window.
    – [ADDED] Scan and Display Features in the Sequence Map window.
    – [ADDED] New “Copy Formatted (Full Seq + Features)”
    – [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct window
    – [ADDED] Warns the user when using the Anti-Parallel, Reverse or Complement commands on only a portion of the sequence
    – [UPDATED] Resizing the Sequence Window is now possible
    – [UPDATED] A pdf file describing Features definition and detection in version 2.1
    – [CORRECTED] Various bugs and interface glitches
    – [CORRECTED] Much improved Linux version (although still not officially supported)

    • Els Melis on September 25, 2017 at 2:04 pm

      Dear Franck,

      Anno 2017, is there a way to import files from CLC Workbench into Serial Cloner?

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