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Drop Selkie hedge mage, it's not really worht it imo and its second ability is too specific to be of much use. Sporeback troll is alright as it gives everything regenerate, but when the ability is on a 2/2 that can be zapped as it comes in to play (before you can graft) it's not worth it for such a high regen cost. Witherscale wurm would be good if you could somehow give it trample, then it would be fantastic as it si it doesn't work all that well and if you graft on to it you'll lose the counters as soon as the -1/-1 counters are put on due to them eliminating each other. Instead replace it with a much much better card. Protean Hydra. With your ability to move counters around you can move them OFF the hydra and then it'll make two more at the end of the turn allowing you to have a fantastic token producer for your deck. Sturdy hatchling is alright, but it doesn't really fit in with the deck too well and you won't be able graft onto it until it loses all it's -1/-1 counters unless you want to risk losing a 1/1 counter permanently. I'd drop the contagion engine, it appears nice at first having both proliferate and -1/-1 counter generation, but it means that you can't ever use the manipulator or experimental kraj's abilities. So you should drop wither them or the engine, up to which one really, but I love the manipulator too much to drop myself especially the synergy with power conduit and other token movers/producers. I'm unsure about the novijen sages, they're good against instant kill effects but beyond that you'll very rarely want to remove 2 counters from your guys just to draw a card. I'd want as many nulltread gargantuans as you can fit in the deck, they're absolutely perfect with graft as you can remove all but one counters from a creature as it comes in then put it on top of your deck to play it out with the full amount again. I'll make more comments later after an update, it's hard to make more comments without seeing what you'll change :)
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You have abit toom uch removal than is really necessary in there I think, for example I think you should drop omnibian, as you'd have to continually tap him to disable one creature when lignify would suit so much better as a permanent solution, the best part being it can be moved about with the guildmages when a bigger threat comes along. Bearing this in mind replacing the snakeforms with pongifies would be good as it is cheaper. Although it lacks instant speed you still have the winged coatls for instant removal as well as various combos to diminish creatures or just take control of them with the maniupulator. I'm not all that fond of assault zeppelid either really, the infilatrator does much better for less mana when grafted. As it stands you could do with dropping a few spells where you can, as this deck is creature based you want to try and keep numbers up so you don't end up with a hand full of spells for only a couple of creatures. I don't think you need quite so many fate transfers as they are an insurance policy for a creature that is about to die, which isn't something you should plan around too much in a graft deck where you'll be half killing your creatures yourself.
*replace the word pngify with lignify, I prefer it myself as I found pongify isn't an enchantment sand so can't be moved around, both are fairly viable though.