Just started playing the game and have read the manual, but I can not figure out how to increase a Perk. I am referring to the Tier 1 Perks like Armsman and Stealth that each have 5 levels you can increase them by. Mine are at 0/5 and everything I have tried such as left mouse clicking does not work. Only mods I am using are SkyUI mod and the unofficial patch.

Any help is appreciated.

you need to increase the skills and level up.
Every character level up gets you 1 perk to spend on a skill you have leveled up.

When you earn enough XP to level up, you'll get an in-game message telling you to access the Skills menu to do so. Go into the skill trees and pick the perk you want; available perks have blue stars, while perks you can't get yet are orange. You don't have to take a perk when you level up; you can save the perk points and use them whenever you wish.

Figured out what the problem was. I was clicking on the text and not the actual colored stars.