They should be the same.
http://www.clamxav.com
Clean, simple-to-use interface
Clearly lists infected files
Free virus definitions (usually updated daily)
Save your favourite scan locations for easy access
Customise the toolbar - or hide it entirely
Send selected files to quarantine or trash with one click
Specify files to exclude using plain text* or by using drag & drop from the Finder
Specify schedules to update virus definitions and perform scans
Use ClamXav Sentry to monitor your hard drive and scan new files as they arrive
Use the bundled ClamAV engine or bring your own installation
Compatible with Mac OS X 10.6, 10.7, 10.8 and OS X 10.9 Mavericks
* You can still use regular expressions if you want the extra flexibility.
Feature not available in the App Store version.
What are the differences between the version of ClamXav available to download here and the version on the Mac App Store?
The App Store version doesn't contain ClamXav Sentry, so it is not able to watch your computer for new files and scan them as they arrive.
There is no engine installation phase as the App Store requirements stipulate that everything must be self-contained within the app.
Virus definition updates are downloaded on a per-user basis.
Updates to the ClamXav app itself are taken care of via the Mac App Store.
Mac OS X 10.6 or greater is required.
The exact same version which is on the Mac App Store can also be downloaded here.
Note: The AppStore version is still at v2.3.6 as v2.6.1 is a substantial rewrite and requires a lot of work to bring the AppStore version up-to-speed. It will happen soon.