An Alternative color is a replacement color of the Skill, Right now 7 skills having alternative colors is Basic Archery, Fire Claw, Bomb Toss, Lighting Spear, Dull Rapier, Ice Armor, and Fiery Explosion, Those are available in Frogidi's Fortunes.
How to get Alternative colors?
You can get Alternative colors by having all 10 Frogidi's Fortunes Skills (Slap, Basic Archery, Fire Claw, Bomb Toss, Lightning Spear, Dull Rapier, Savage Hit, Barrage, Ice Armor and Fiery Explosion). That will cost 100 Tokens. After having all of Frogidi's Fortunes Skills you can still spend 10 Tokens. So that for a random Alternative color of a random 7(Basic Archery, Fire Claw, Bomb Toss, Lighting Spear, Dull Rapier, Ice Armor, and Fiery Explosion) Frogidi's Fortunes Skills.
There 122 Alternative colors in total, which is cost 1220 Tokens to unlock every single Alternative color. The most valuable Alternative colors are Purple, which is an Alternative color to be like a Corruption Skill (Doesn't do anything with damage, because is just an Alternative color).