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Website usage notes: Windows pages are green; UNIX/Mac pages are blue. If you're on the wrong page, choose your platform in the Navigation bar on the left.


NEW! Scriptome programs - Change a FASTA file to tabular format by typing the following on the (UNIX, Mac or Windows) command line:

Scriptome -t change_fasta_to_tab seqs.fasta >

The program will retrieve tool code from the web, then run it. (There's also a no-Internet version.) Available on the Resources page. (1/2007)

NEW! New Tools

NEW! Expandable Perl code - one of our most popular requests. Click the "Expand code" button next to any tool's code for a much more readable view.

NEW! Tips and Resource Pages - The Tips page features quick advice on using tools, writing protocols, and general data management. The Resources page features downloads, mailing lists, and other links. (1/2007)



You do not need to install or download these tools. (Windows users need Perl, a one-click install.)

  1. Pick a tool category from the Navigation bar on the left (or links below).

  2. Find a tool by browsing the expandable table of contents.

  3. Change parameters and input/output filenames using the mini-form.

  4. Select the code in the dashed-line, blue or green box using the mouse.

  5. Copy and paste the code into a terminal window. (How do I open a terminal window?.)

  6. Hit Enter to run the tool.

There are more detailed instructions and a sample tool available.

Tool Categories

  • Calculate simple statistics about the data, like sums, counts, lengths...

  • Change (reformat) files or lines

  • Choose (filter) columns, lines, or records

  • Fetch data from local or Internet sources

  • Merge files together

  • Sort lines alphabetically, numerically, based on a given column...

Tools for more experienced users

Download programs that allow you to run Scriptome tools from the command line, with no web browsing required.


A Scriptome protocol is a series of steps that solve a data manipulation problem. Each step is carried out by running a Scriptome tool - often by running it on the output generated by an earlier step.

Help and More Information

Visit the help pages for:

  • Overview of the project

  • Help on using the Scriptome's tools and protocols

  • Frequently Asked Questions

  • Principles behind the Scriptome (in case you're curious)

  • Resources: Scriptome programs to download, mailing lists, links, and developer information

  • Tips on using tools, writing protocols, and data management

All of these pages are available in the "Information" section in the navbar on the left.

Developers Wanted!

If you are interested in the development of the Scriptome, read the Scriptome Manifesto, and then go to the Scriptome development page at

Submit code for new tools or protocols to Amir Karger.

Old News

NEW! No More Backspace - Type parameters and input/output filenames into a "form" just above each tool. The text in the colored box will be magically updated. Then just cut, paste, and hit Enter. See a working example or just try your favorite tool. (7/2006)

NEW! Tool Cleanup - Several of your favorite tools have been cleaned up and made more user friendly. They now have better output messages and the code is a bit simpler. Much of the work was done by volunteer Jason Konrad. Thanks, Jason! (7/2006)

New Calc Tools - The following tools have been added:

In addition, calc_num_lines and calc_num_fasta_records have been updated so that they also work on Windows. See the Calc page for more details. (2/2006)

New FASTA Protocols - Several protocols which filter or reformat FASTA files have been added to the Sequences page. (2/2006)

Windows Scriptome There are now Scriptome tools available for Windows. (10/2005)

Better Tool Browsing Collapsible table of contents for easier reading, Quickbrowse menu to find known tools faster (10/2005)


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