
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:41 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip" (19 taxa, 347 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
GTRG	44	-1199.6817	2500.4760	0.7101	0.7101
GTRIG	45	-1199.6813	2503.1168	0.1896	0.8997
GTRI	44	-1201.8764	2504.8654	0.0791	0.9788
HKYG	40	-1209.4964	2509.7118	0.0070	0.9859
SYMG	41	-1208.4199	2510.1317	0.0057	0.9915
HKYIG	41	-1209.4957	2512.2832	0.0019	0.9935
K2PG	37	-1214.6500	2512.4003	0.0018	0.9953
SYMIG	42	-1208.4195	2512.7205	0.0016	0.9969
HKYI	40	-1211.2543	2513.2275	0.0012	0.9981
SYMI	41	-1210.5259	2514.3435	0.0007	0.9988
K2PIG	38	-1214.6477	2514.9187	0.0005	0.9993
GTR	43	-1208.5148	2515.5180	0.0004	0.9997
K2PI	37	-1216.3732	2515.8467	0.0003	1.0000
SYM	40	-1216.9619	2524.6427	0.0000	1.0000
HKY	39	-1218.4677	2525.0983	0.0000	1.0000
K2P	36	-1224.3450	2529.2835	0.0000	1.0000
F81G	39	-1238.1054	2564.3737	0.0000	1.0000
JC69G	36	-1242.6400	2565.8735	0.0000	1.0000
F81IG	40	-1238.1047	2566.9283	0.0000	1.0000
F81I	39	-1239.6656	2567.4941	0.0000	1.0000
JC69IG	37	-1242.6389	2568.3781	0.0000	1.0000
JC69I	36	-1244.1949	2568.9834	0.0000	1.0000
F81	38	-1247.0350	2579.6933	0.0000	1.0000
JC69	35	-1251.7153	2581.5336	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1199.6817	2487.3634	0.6713	0.6713
GTRIG	45	-1199.6813	2489.3627	0.2470	0.9183
GTRI	44	-1201.8764	2491.7529	0.0748	0.9931
SYMG	41	-1208.4199	2498.8399	0.0022	0.9952
HKYG	40	-1209.4964	2498.9929	0.0020	0.9972
SYMIG	42	-1208.4195	2500.8390	0.0008	0.9980
HKYIG	41	-1209.4957	2500.9914	0.0007	0.9988
HKYI	40	-1211.2543	2502.5085	0.0003	0.9991
GTR	43	-1208.5148	2503.0295	0.0003	0.9994
SYMI	41	-1210.5259	2503.0517	0.0003	0.9996
K2PG	37	-1214.6500	2503.3000	0.0002	0.9999
K2PIG	38	-1214.6477	2505.2953	0.0001	1.0000
K2PI	37	-1216.3732	2506.7464	0.0000	1.0000
SYM	40	-1216.9619	2513.9237	0.0000	1.0000
HKY	39	-1218.4677	2514.9354	0.0000	1.0000
K2P	36	-1224.3450	2520.6900	0.0000	1.0000
F81G	39	-1238.1054	2554.2109	0.0000	1.0000
F81IG	40	-1238.1047	2556.2094	0.0000	1.0000
JC69G	36	-1242.6400	2557.2800	0.0000	1.0000
F81I	39	-1239.6656	2557.3313	0.0000	1.0000
JC69IG	37	-1242.6389	2559.2777	0.0000	1.0000
JC69I	36	-1244.1949	2560.3899	0.0000	1.0000
F81	38	-1247.0350	2570.0699	0.0000	1.0000
JC69	35	-1251.7153	2573.4307	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1214.6500	2645.7250	0.7837	0.7837
K2PI	37	-1216.3732	2649.1714	0.1399	0.9235
K2PIG	38	-1214.6477	2651.5696	0.0422	0.9657
HKYG	40	-1209.4964	2652.9659	0.0210	0.9867
HKYI	40	-1211.2543	2656.4815	0.0036	0.9903
SYMG	41	-1208.4199	2656.6622	0.0033	0.9936
GTRG	44	-1199.6817	2656.7337	0.0032	0.9968
HKYIG	41	-1209.4957	2658.8137	0.0011	0.9979
K2P	36	-1224.3450	2659.2657	0.0009	0.9988
SYMI	41	-1210.5259	2660.8741	0.0004	0.9992
GTRI	44	-1201.8764	2661.1232	0.0004	0.9996
SYMIG	42	-1208.4195	2662.5106	0.0002	0.9998
GTRIG	45	-1199.6813	2662.5823	0.0002	0.9999
HKY	39	-1218.4677	2665.0591	0.0000	1.0000
SYM	40	-1216.9619	2667.8967	0.0000	1.0000
GTR	43	-1208.5148	2668.5505	0.0000	1.0000
JC69G	36	-1242.6400	2695.8557	0.0000	1.0000
JC69I	36	-1244.1949	2698.9656	0.0000	1.0000
JC69IG	37	-1242.6389	2701.7028	0.0000	1.0000
F81G	39	-1238.1054	2704.3345	0.0000	1.0000
F81I	39	-1239.6656	2707.4549	0.0000	1.0000
JC69	35	-1251.7153	2708.1570	0.0000	1.0000
F81IG	40	-1238.1047	2710.1824	0.0000	1.0000
F81	38	-1247.0350	2716.3443	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip = 1 - 347;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_1367.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

