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Alisim problem with the Gamma distribution when using mixture models #238

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Boussau opened this issue Sep 30, 2022 · 0 comments
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Boussau commented Sep 30, 2022

When trying to simulate an alignment with a mixture model and a continuous Gamma distribution on rate heterogeneity across sites, we encountered a problem.
We could not specify the continuous distribution: by default it had 4 categories, and it used a default alpha value of 1.0. Our command:
iqtree2 --alisim alignment_aa.fasta -m LG+C60+GC{0.5} -t tree.nwk
was apparently interpreted as:
LG+POISSON+G+FMIX{C60pi1:1:0.0169698865,C60pi2:1:0.0211683374,C60pi3:1:0.0276589079,C60pi4:1:0.0065675964,C60pi5:1:0.0141221416,C60pi6:1:0.0068774834,C60pi7:1:0.0146909701,C60pi8:1:0.0067225777,C60pi9:1:0.0018396660,C60pi10:1:0.0102547197,C60pi11:1:0.0230896163,C60pi12:1:0.0057941033,C60pi13:1:0.0125394534,C60pi14:1:0.0204526478,C60pi15:1:0.0070629602,C60pi16:1:0.0117982741,C60pi17:1:0.0068334668,C60pi18:1:0.0433775839,C60pi19:1:0.0318278731,C60pi20:1:0.0222546108,C60pi21:1:0.0102264969,C60pi22:1:0.0150545891,C60pi23:1:0.0134159878,C60pi24:1:0.0148552065,C60pi25:1:0.0239111516,C60pi26:1:0.0128776278,C60pi27:1:0.0222318842,C60pi28:1:0.0247444742,C60pi29:1:0.0214274810,C60pi30:1:0.0115001882,C60pi31:1:0.0076017389,C60pi32:1:0.0130258568,C60pi33:1:0.0093701965,C60pi34:1:0.0467194264,C60pi35:1:0.0441940314,C60pi36:1:0.0322263154,C60pi37:1:0.0402999891,C60pi38:1:0.0150234227,C60pi39:1:0.0104589903,C60pi40:1:0.0214742395,C60pi41:1:0.0154957836,C60pi42:1:0.0101789953,C60pi43:1:0.0227980379,C60pi44:1:0.0123204539,C60pi45:1:0.0066777583,C60pi46:1:0.0004150083,C60pi47:1:0.0344385130,C60pi48:1:0.0113663379,C60pi49:1:0.0127143049,C60pi50:1:0.0124323741,C60pi51:1:0.0262124415,C60pi52:1:0.0064994957,C60pi53:1:0.0103203293,C60pi54:1:0.0142463512,C60pi55:1:0.0215600067,C60pi56:1:0.0199150700,C60pi57:1:0.0038964200,C60pi58:1:0.0113448855,C60pi59:1:0.0128595846,C60pi60:1:0.0117656776}+G{0.5} (notice the extra +G at the beginning of the model definition.)

We were able to use the full model specification to change the alpha parameter to any value, by removing the extra +G, but we never managed to get the continuous gamma distribution to work.

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