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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?

  4. Edgardo Rivera Delgado on May 13, 2010 at 1:47 pm

    I must agree. I downloaded this program a while ago and it’s been really helpful. I like the virtual restriction digest. I can visually compare my gel band sizes to the virtual band sizes and create my own customized ladder. You can do almost anything you can do in a commercial software. All of this for free. Thanks for sharing Serial Cloner!

  5. Franck Perez on May 13, 2010 at 12:47 pm

    Hi Cristian,

    yes, sorry. It is taking more time than expected because of so many other stuff to get going in the lab. The version is ready. I just need time to write a small documentation and to update my web site… Hopefully, soon !

  6. Cristian on April 12, 2010 at 8:00 pm

    Hi Franck,

    I just wanted to let you know that the Serial Cloner is a great Software, way better than the one which everyone used in the past and now is not freeware nowadays..I don’t even want to pronounce its name anymore…because some guys let you first use it and exactly when you need it mostly, they decide to trade it for lots of money. And then you are in such a bad position, that even if the lab doesn’t have enough money, you are forced to buy it because you think there is nothing out there, which can keep up with their bloody software…well, they should know that there is something out there and that is Serial Cloner. I hope only one thing: that this software will be freeware forever…One question: when are you going to launch the next version? The one with customized scanning? Thanks and keep up the great work,Cris

  7. Franck on February 28, 2010 at 9:39 pm

    Hi Sebastian,

    do not hesitate to contact me at using the email address indicated on my web site.
    Anyway, sorry to learn that you had a pb using Serial Cloner. Sometimes, the pref file gets corrupted. Please try to start the soft while pressing [CTRL] and [SHIFT]. Serial Cloner should ask you whether it may reset the prefs. Say ‘yes’.
    I hope it will solve your problem.

  8. Sebastian on February 3, 2010 at 4:35 pm

    Hi Franck,
    thanks in advance for this nice piece of software.
    I am running Serial Cloner2.0 on WinXP and was about to create a customized DNA Ladder with the “virtual cutter” tool,(which worked fine so far) when it suddenly crashed(for the first time). The program is stil useable since, but each time i try to start the virtualcutter the same bug occurs.
    **error message**
    “An exception of class OutOfBoundsException was not handled. The application must shut down.”

    Which is a pity since i really did appreciate this feature.
    Re-installing SC2.0 didnt helped as well.

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