The output file for the selected evolutionary models by ModelFinder is extremely confusing.
This is what I got:
PartitionModelPlen: 58s+tefcdn1_1+tefcdn1_2+tefcdn3_3+rpb1cdn1_1!ModelDNA!rates: 1, 5.564746318, 1, 1, 5.564746318, 1 58s+tefcdn1_1+tefcdn1_2+tefcdn3_3+rpb1cdn1_1!RateGammaInvar!gamma_shape: 0.5397338853 58s+tefcdn1_1+tefcdn1_2+tefcdn3_3+rpb1cdn1_1!RateGammaInvar!p_invar: 0.8458780356 58s+tefcdn1_1+tefcdn1_2+tefcdn3_3+rpb1cdn1_1!RateInvar!p_invar: 0.9243709196 its1+its2!ModelDNA!rates: 1, 3.279709161, 1, 1, 3.279709161, 1 its1+its2!RateGamma!gamma_shape: 0.5812459045 its1+its2!RateGammaInvar!gamma_shape: 0.7562637271 its1+its2!RateGammaInvar!p_invar: 0.100810994 its1+its2!RateInvar!p_invar: 0.2958478399 linked_alpha: -1 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!ModelDNA!rates: 1.268009068, 3.758645355, 1.742912459, 1.051485565, 9.551263492, 1 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFree2!prop: 0.89266371, 0.10733629 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFree2!rates: 0.2867402659, 6.93183424 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFree3!prop: 0.7685918045, 0.1740954144, 0.05731278108 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFree3!rates: 0.1374098043, 1.848702337, 9.989697589 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFreeInvar2!p_invar: 0.5967015024 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFreeInvar2!prop: 0.340695949, 0.06260254859 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateFreeInvar2!rates: 1.163650563, 9.6409648 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateGamma!gamma_shape: 0.1889561985 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateGammaInvar!gamma_shape: 0.5118992701 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateGammaInvar!p_invar: 0.5199632601 lsu+tefcdn2_1+tefcdn2_2+tefcdn3_2+rpb1cdn1_2+rpb1cdn2_2+rpb1cdn2_3+rpb1cdn3_1+rpb1cdn3_3!RateInvar!p_invar: 0.7137626954 part_rates: 1.345377855, 0.03424426052, 0.2621830198, 1.598758477, 4.977392704, 2.988147018, 0.8544574211 rpb1cdn1_3+rpb1int2!ModelDNA!rates: 1.072549288, 2.647505525, 1.727387683, 0.9424122206, 4.884589727, 1 rpb1cdn1_3+rpb1int2!RateGamma!gamma_shape: 0.5051536071 rpb1cdn1_3+rpb1int2!RateGammaInvar!gamma_shape: 0.9648772513 rpb1cdn1_3+rpb1int2!RateGammaInvar!p_invar: 0.2207490473 rpb1cdn1_3+rpb1int2!RateInvar!p_invar: 0.4294853308 rpb1int1+rpb1cdn2_1+rpb1int3+rpb1cdn3_2+rpb1int4!ModelDNA!rates: 1, 4.809816234, 1, 1, 4.809816234, 1 rpb1int1+rpb1cdn2_1+rpb1int3+rpb1cdn3_2+rpb1int4!RateGammaInvar!gamma_shape: 4.299199339 rpb1int1+rpb1cdn2_1+rpb1int3+rpb1cdn3_2+rpb1int4!RateGammaInvar!p_invar: 0.1096089666 rpb1int1+rpb1cdn2_1+rpb1int3+rpb1cdn3_2+rpb1int4!RateInvar!p_invar: 0.1225317005 tefcdn1_3+tefcdn2_3+tefcdn3_1!ModelDNA!rates: 1, 9.665980115, 1, 1, 9.665980115, 1 tefcdn1_3+tefcdn2_3+tefcdn3_1!RateGamma!gamma_shape: 0.6601082161 tefcdn1_3+tefcdn2_3+tefcdn3_1!RateGammaInvar!gamma_shape: 1.401759531 tefcdn1_3+tefcdn2_3+tefcdn3_1!RateGammaInvar!p_invar: 0.1969112862 tefcdn1_3+tefcdn2_3+tefcdn3_1!RateInvar!p_invar: 0.286122086 tefint1+tefint2!ModelDNA!rates: 1, 2.753516728, 1, 1, 2.753516728, 1 tefint1+tefint2!RateFreeInvar2!p_invar: 0.1043790369 tefint1+tefint2!RateFreeInvar2!prop: 0.1895112802, 0.7061096829 tefint1+tefint2!RateFreeInvar2!rates: 0.3658744754, 1.3180143 tefint1+tefint2!RateGammaInvar!gamma_shape: 3.722032796 tefint1+tefint2!RateGammaInvar!p_invar: 0.1068231271 tefint1+tefint2!RateInvar!p_invar: 0.1074103909
And I'm trying to make sense of it all for building my MrBayes script. Could anyone help me out to understand what are the parameters that I should include in my script? I'd be greatly appreciated, this is very confusing.
Like, should I use the RateGamma! or RateGammaInvar! for the shapepr and pinvar?
What is RateFree2! RateFree3? RateFreeInvar2! ???