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
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 > seqs.tab
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
You do not need to install or download these tools.
(Windows users need Perl, a one-click install.)
Pick a tool category from the Navigation bar on the left (or links below).
Find a tool by browsing the expandable table of contents.
Change parameters and input/output filenames using the mini-form.
Select the code in the dashed-line, blue or green box using the mouse.
Copy and paste the code into a terminal window.
(How do I open a terminal window?.)
Hit Enter to run the tool.
There are more detailed instructions and a sample tool
Calculate simple statistics about the data, like sums, counts,
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...
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.
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.
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.
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.
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)