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10 links: Free PC Software for Molecular Biologists

Here is a list of 10 pieces of great molecular biology software for PC users that I hope you will find useful. I am not a regular PC user myself so I have not tested all of these out so if any of these are no good, or if you have any favorites you’d like to add please let me know by leaving a comment below. If you are a Mac user, click here for the Mac list.

1. Serial Cloner
Serial Cloner is fantastic all-in-one workbench; import and manipulate sequences, construct plasmid and restriction site maps, determine %GC and fragment TM, extract and ligate fragments, perform virtual PCR… and lots more, all in one window using a very intuitive graphical interface.

2. Artemis
Artemis is a very user friendly DNA sequence viewer and annotation tool released by the Sanger center. It is the main tool used by the guys at the Sanger Centre for sequence annotation… and they do A LOT of sequence annotation

3. Molecular Weight Calculator
This free molecular weight calculator from the NCRR allows easy calculation of molecular weights from formulae and amino acid sequences, and does some other pretty useful stuff too.

4. SeqVerter
A convenient sequence format converter application that can be used for… you’ve guessed it… converting sequences between formats. A free part of the commercial GeneStudio package.

5. Geneious
Geneious is a software package of genome & proteome research tools for protein, DNA or molecular visualization, literature searching and storage…and more. The Pro version does LOTS more.

6. Foxit Reader
Foxit Reader is a PDF viewer, reader and annotator. In terms of file size it is an amazing 10 times smaller than Adobe Acrobat (2 MB compared to Acrobat’s 20M), but it is packed with many more features. I especially love the annotation capability that allows you to add typed notes, highlight text or add graphics. Use it, save paper and save the rainforests!

7. Fast PCR
Fast PCR is a really nice piece of software for primer design and in silico PCR. Free for academic and non-commercial use only.

8. ApE
ApE is an all-in-one plasmid and sequence workbench. Sequences can be uploaded to ApE manually, direct from the NCBI database or from ABI chromatogram traces. ApE can be used for sequence annotation, restriction mapping, primer design and sequence alignment. A great all round tool.

9. Cn3D
Cn3D… say it out loud… “see in 3D”. This great piece of software from NCBI is a sequence viewer with a difference. Not only does it perform 2D alignments, it also allows the user to see the position residues in the 3D protein sequence. Great for mutagenesis studies.

10. BioToolKit
This is one packed toolkit! Primer design, antibody design, microarray analysis, calculators for molecular weight, molar concentration and OD, centrifguation speed converter, label printing templates… and much more! Phew!

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2 Comments

  1. Julien Dal Col on April 7, 2016 at 4:13 pm

    Benchling is missing. How is this possible?

  2. EMIL on April 7, 2016 at 4:05 pm

    WebDSV (http://www.molbiotools.com/WebDSV/) is another useful molecular biology freeware. It offers DNA sequence editing, sequence feature management, primer design, map drawing, and more. All can be done conveniently in an internet browser window without any installation and even without registration. Work can be saved in the universally compatible GenBank files.

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