Are you asking how to run a perl script from within a PHP script? Don't you have a book or manual or some other documentation about PHP that tells you how to run some other program from within a PHP script?

When you figure out how to do that, it will probably involve passing a "command line string" to some PHP function for running a command line, and you'll have the option of putting "command line arguments" in that string, including, for example, the name of a perl script, and anything that the perl script needs in its @ARGV array on start-up (e.g. one or more file names, any optional flags, etc).

Depending on what the perl script happens to be (I hope you have a man page or other docs on that as well), you'll need to figure out what you need to put into the command line string in your php script.

E.g. you might need to save the ">seqN" labels and strings of letters in a file, and include the file name in the command line string that runs the perl script.

This is not a place to ask questions about how to do things with PHP. If you're looking for help with a perl script, tell us what the script needs to do, show us what you've tried, and make it clear what sort of problem you're having.

By the way, if you put "<code>" and "</code>" around your data, it will show up correctly in your post. You can update you post to fix that.