A run does not offer you every skill. Of the 187 skills that can appear, 126 are always in the pool and 61 are behind a rule: they need something else first, or they are shut out by a skill you already took. This is every one of those rules.

1The four rules

RuleWhat it does
Element countOnce you hold 2 skills of an element, the rest of that element opens up. Four skills need only 1. This is the big one: 51 skills are behind it.
PrerequisiteA few skills need one specific skill first, on top of any element count.
LockoutTaking one skill permanently removes its opposite for the rest of the run. It works both ways round.
PetsTwo skills only appear if you have pets.
The count is at least, not exactly, and it counts skills you have learned this run. Nothing ever closes again once it opens, except through a lockout.

2Choices that lock the other out 8 pairs

Take either one and the other is gone for the rest of the run. These are the only irreversible picks in the pool.

Adrenaline Rush
After applying Wound 10 times, fully fill your Ultimate Bar
LOCKS
Burning Rage
You can no longer gain Ultimate Charge, but all your Cleaves are replaced with Steel Cyclone
Beefcake
Max HP +55%, ATK -30%
LOCKS
Glass Cannon
ATK +55%, Max HP -30%
Charged Battery
Your Bolts deal no damage but grant 1 stack of Charged Battery. After your Ultimate, cast Mega Bolt, dealing more damage
LOCKS
High Voltage
Each Bolt increases your Lightning DMG by +8% | +12% for 2 turns.
Cleave Mastery
Cleave DMG +130%, but no longer applies Wound.
LOCKS
Wound Mastery
Wound can now stack up to 20 | 30 times.
Deadly Stars
Shuriken DMG +125%, but Shurikens no longer trigger other effects.
LOCKS
Heal Shuriken
Every 2 rounds, throw 1 Shuriken. All Shurikens have a chance to heal you a bit. | Chance increased
Deadly Stars
Shuriken DMG +125%, but Shurikens no longer trigger other effects.
LOCKS
Poison Shuriken
Every 2 rounds, throw 1 Shuriken. All Shurikens have a chance to apply Poison. | Chance increased
Deadly Stars
Shuriken DMG +125%, but Shurikens no longer trigger other effects.
LOCKS
Wound Shuriken
Every 2 rounds, throw 1 Shuriken. All Shurikens have a chance to apply Wound. | Chance increased
Warrior
Physical DMG +50%, Weapon Attack DMG +50%, Magical DMG -50%
LOCKS
Wizard
Magical DMG +50%, Skill DMG +50%, Physical DMG -30%
Deadly Stars is the one to think about. It is locked out by Heal Shuriken and Poison Shuriken and Wound Shuriken, so two different picks can take it off the table, and it is the only skill in the game with more than one thing that shuts it out.

3What each element opens 2 skills of that element, unless marked

Pick 2 skills of an element and everything below unlocks at once. The four in green need only 1, so they are the cheapest way into a tree.

Fire8 skills
Blazing FrenzyDeadly FlamesFire LordFire MasteryFirestarterFlame StrikeInfernoMeltdown
Ice8 skills
Enervating ColdEvercoldFreezing ColdFrost NovaFrost StrikeFrostbiteIce MasteryIce Spikes
Lightning9 skills
Charged BatteryEnergizing CurrentHigh VoltageLightning MasteryOverloadRepeated BoltStatic DischargeThunder GodThunderstorm
Poison8 skills
ContagionCrippling CloudDeep VenomEnvenomFesterOutbreakPoison MasteryVenom Burst
Wound9 skills
Adrenaline RushBerserkBloodlustBurning RageCleave MasteryLicking WoundsSteel CycloneThrill of BattleWound Mastery
Shuriken9 skills
Deadly StarsDeath LotusElemental StarsFuma ShurikenQuick ThrowShadow PartnerShuricoinsShuriken MasteryThousand Cuts
The four that need only one: Elemental Stars, Frostbite, Overload, Shuricoins. Everything else on this page needs two.

4Skills that need a specific skill first

Take thisand these become possible
CleaveBerserk (also needs 2 Wound)
Steel Cyclone (also needs 2 Wound)
Thrill of Battle (also needs 2 Wound)
Flame StrikeMeteor
These stack with the element count rather than replacing it, so Meteor wants Flame Strike and Flame Strike itself wants 2 Fire skills. That is the longest chain in the game: 2 Fire, then Flame Strike, then Meteor.

5Needs pets

SkillWhat it does
Better With FriendsPet DMG +40%
Special ExperimentWhen your Pets attack, they will apply 1 | 2 stack of Poison.

6Rules the game does not actually enforce 10 of 12 relationships are incomplete

Everything above is what the rules say. This is what the game does, and they are not the same once the skill tree is involved. Researching a skill to Lv. 2 gives you a different card, and the rules were written against the Lv. 1 card. The game matches the exact card, so a Lv. 2 in your tree quietly drops you out of the rule.

Flame Strike used to be a trap and no longer is. Meteor once accepted only the Lv. 1 card, so researching Flame Strike Lv. 2 locked Meteor out of your run. It now accepts either card, so the research is safe. Section 7 has the version it changed in.
The rest go the other way and hand you something. 7 of the lockouts above stop working if the Lv. 2 card is the one you hold, so pairs the game means to be either-or become both-at-once. Beefcake Lv. 2 does not lock Glass Cannon, and the same is true of Warrior and Wizard, and of Cleave Mastery and Wound Mastery.
Every incomplete link, per card
RelationshipKindMissingThis card……does not list
Beefcake and Glass Cannonexclusion8 of 32BeefcakeGlass Cannon Lv. 2
BeefcakeGlass Cannon Lv. 2+
Beefcake+Glass Cannon Lv. 2
Beefcake+Glass Cannon Lv. 2+
Glass CannonBeefcake Lv. 2
Glass CannonBeefcake Lv. 2+
Glass Cannon+Beefcake Lv. 2
Glass Cannon+Beefcake Lv. 2+
Charged Battery and High Voltageexclusion2 of 8Charged BatteryHigh Voltage Lv. 2
Charged BatteryHigh Voltage Lv. 2+
Cleave Mastery and Wound Masteryexclusion10 of 16Cleave MasteryWound Mastery+
Cleave Mastery+Wound Mastery+
Cleave Mastery Lv. 2Wound Mastery+
Cleave Mastery Lv. 2+Wound Mastery+
Wound MasteryCleave Mastery+
Wound MasteryCleave Mastery Lv. 2
Wound MasteryCleave Mastery Lv. 2+
Wound Mastery+Cleave Mastery+
Wound Mastery+Cleave Mastery Lv. 2
Wound Mastery+Cleave Mastery Lv. 2+
Deadly Stars and Heal Shurikenexclusion7 of 8Deadly StarsHeal Shuriken
Deadly StarsHeal Shuriken+
Deadly Stars Lv. 2Heal Shuriken
Deadly Stars Lv. 2Heal Shuriken+
Heal ShurikenDeadly Stars
Heal ShurikenDeadly Stars Lv. 2
Heal Shuriken+Deadly Stars Lv. 2
Deadly Stars and Poison Shurikenexclusion7 of 8Deadly StarsPoison Shuriken
Deadly StarsPoison Shuriken+
Deadly Stars Lv. 2Poison Shuriken
Deadly Stars Lv. 2Poison Shuriken+
Poison ShurikenDeadly Stars
Poison ShurikenDeadly Stars Lv. 2
Poison Shuriken+Deadly Stars Lv. 2
Deadly Stars and Wound Shurikenexclusion7 of 8Deadly StarsWound Shuriken
Deadly StarsWound Shuriken+
Deadly Stars Lv. 2Wound Shuriken
Deadly Stars Lv. 2Wound Shuriken+
Wound ShurikenDeadly Stars
Wound ShurikenDeadly Stars Lv. 2
Wound Shuriken+Deadly Stars Lv. 2
Warrior and Wizardexclusion8 of 32WarriorWizard Lv. 2
WarriorWizard Lv. 2+
Warrior+Wizard Lv. 2
Warrior+Wizard Lv. 2+
WizardWarrior Lv. 2
WizardWarrior Lv. 2+
Wizard+Warrior Lv. 2
Wizard+Warrior Lv. 2+
Berserk and Cleaveprerequisite1 of 2BerserkCleave+
Steel Cyclone and Cleaveprerequisite3 of 4Steel CycloneCleave+
Steel Cyclone+Cleave
Steel Cyclone+Cleave+
Thrill of Battle and Cleaveprerequisite1 of 2Thrill of BattleCleave+
Read the last two columns as one sentence: the card on the left does not name the card on the right, so holding the right one does not trigger the rule. A relationship is only fully wired when every card of each side names every card of the other, because either side can be the one you are offered second. Two of the 12 relationships in the game are wired that way today.
The + rows in that table are a different case from the Lv. 2 ones and are listed for completeness. Whether they change anything you would notice in a run has not been tested, so treat them as data to check rather than as bugs you can use.

7What the devs have fixedchanges between game versions

This page is about relationships the game does not fully enforce, so the useful question is whether they are getting fixed. Each entry below is a change between two game versions, read from the files rather than from patch notes.

Version by version
VersionRelationshipKindChangeMissing links
0.560Meteor and Flame Strikeprerequisitefixed (now fully wired)1 of 2 → 0 of 2
Only versions we still hold an extraction for can be compared, so this list starts where our records do rather than at the first release.
Every rule on this page is read out of the game files and checked against the code that decides which skills a run can offer you. One thing it cannot show: you can switch an individual skill off yourself so it is never offered, and that setting is on your device rather than in the game data.