Usually you don't
What does slow mean or behavior, what apps.
I wish I had $1 for every such question I see, more so on OS X forum. But also earlier today -
Do a clean install after you format a new drive and then after all the updates and insuring it works use Setup Assistant.
There is no magic bullet.
Maybe do two Safe Boots. Repair the disk drive. =
Maybe you already deleted all the browser cache.
Move the home folder to another drive.
Add more RAM. Buy an SSD.
Unplug and disconnect all the devices other than kb and mouse.
Mac Pro normally don't slow down over time unless you have crashed and froze and haven't repaired the boot drive. Or you have been using the same system drive through two full OS upgrades. A new OS is great time to buy and use a new drive and keep the old one handy as dual boot backup.
Try using Disk Utility to do a Disk Repair, as shown in this link, while booted up on your install disk.
You could have some directory corruption. Let us know what errors Disk Repair reports and if DU was able to repair them. This could just be a start in repairs and you may need a better utility to finish the job.
Then Repair Permissions.
No need to report any Permissions errors........we all get them.