How do you profile your PHP applications?

I know that in our websites we benchmark queries made to the database instead of the PHP performance.

Another thing is a microtime(true) in the beginning and end of your script, and comparing the time, then change some code to see if it produces a slowdown.

But it really depends on what you're doing with your application. It this for a website, crawler, etc?

Historically, github.com/lox/xhprof has been the solution to profile PHP applications. However, it hasn't been updated in many years. pecl.php.net/package/xhprof will give you more info about it.

Blackfire.io does a great job. Pretty easy to setup. It has a trial, but it's not very expensive thereafter.