
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:36 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/chr1_19426.phylip" (19 taxa, 303 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	-1221.1330	2545.6148	0.6901	0.6901
GTRIG	45	-1221.1047	2548.3184	0.1786	0.8686
GTRI	44	-1222.8177	2548.9842	0.1280	0.9966
HKYG	40	-1232.5237	2557.5664	0.0018	0.9984
SYMG	41	-1232.2236	2559.6425	0.0006	0.9990
HKYIG	41	-1232.4325	2560.0603	0.0005	0.9995
HKYI	40	-1234.6849	2561.8888	0.0002	0.9997
SYMIG	42	-1232.1726	2562.2374	0.0002	0.9999
SYMI	41	-1234.2893	2563.7740	0.0001	1.0000
K2PG	37	-1240.8279	2566.2671	0.0000	1.0000
K2PIG	38	-1240.7206	2568.6684	0.0000	1.0000
K2PI	37	-1243.2205	2571.0524	0.0000	1.0000
GTR	43	-1247.6418	2595.8937	0.0000	1.0000
HKY	39	-1259.0094	2607.8819	0.0000	1.0000
SYM	40	-1260.1819	2612.8829	0.0000	1.0000
K2P	36	-1268.7976	2619.6102	0.0000	1.0000
F81G	39	-1271.0001	2631.8634	0.0000	1.0000
F81IG	40	-1270.8852	2634.2895	0.0000	1.0000
F81I	39	-1273.1663	2636.1958	0.0000	1.0000
JC69G	36	-1277.9851	2637.9853	0.0000	1.0000
JC69IG	37	-1277.8873	2640.3859	0.0000	1.0000
JC69I	36	-1280.2130	2642.4410	0.0000	1.0000
F81	38	-1296.5492	2680.3256	0.0000	1.0000
JC69	35	-1303.9081	2687.2545	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1221.1330	2530.2660	0.6388	0.6388
GTRIG	45	-1221.1047	2532.2094	0.2418	0.8806
GTRI	44	-1222.8177	2533.6354	0.1185	0.9991
HKYG	40	-1232.5237	2545.0473	0.0004	0.9995
SYMG	41	-1232.2236	2546.4471	0.0002	0.9997
HKYIG	41	-1232.4325	2546.8649	0.0002	0.9999
SYMIG	42	-1232.1726	2548.3451	0.0001	0.9999
HKYI	40	-1234.6849	2549.3697	0.0000	1.0000
SYMI	41	-1234.2893	2550.5786	0.0000	1.0000
K2PG	37	-1240.8279	2555.6558	0.0000	1.0000
K2PIG	38	-1240.7206	2557.4411	0.0000	1.0000
K2PI	37	-1243.2205	2560.4411	0.0000	1.0000
GTR	43	-1247.6418	2581.2836	0.0000	1.0000
HKY	39	-1259.0094	2596.0187	0.0000	1.0000
SYM	40	-1260.1819	2600.3639	0.0000	1.0000
K2P	36	-1268.7976	2609.5952	0.0000	1.0000
F81G	39	-1271.0001	2620.0003	0.0000	1.0000
F81IG	40	-1270.8852	2621.7704	0.0000	1.0000
F81I	39	-1273.1663	2624.3327	0.0000	1.0000
JC69G	36	-1277.9851	2627.9702	0.0000	1.0000
JC69IG	37	-1277.8873	2629.7746	0.0000	1.0000
JC69I	36	-1280.2130	2632.4259	0.0000	1.0000
F81	38	-1296.5492	2669.0984	0.0000	1.0000
JC69	35	-1303.9081	2677.8163	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1240.8279	2693.0639	0.3281	0.3281
HKYG	40	-1232.5237	2693.5966	0.2514	0.5795
GTRG	44	-1221.1330	2693.6702	0.2423	0.8218
GTRI	44	-1222.8177	2697.0396	0.0449	0.8668
K2PI	37	-1243.2205	2697.8492	0.0300	0.8968
HKYI	40	-1234.6849	2697.9190	0.0290	0.9257
K2PIG	38	-1240.7206	2698.5630	0.0210	0.9467
SYMG	41	-1232.2236	2698.7102	0.0195	0.9662
HKYIG	41	-1232.4325	2699.1279	0.0158	0.9820
GTRIG	45	-1221.1047	2699.3274	0.0143	0.9964
SYMI	41	-1234.2893	2702.8416	0.0025	0.9988
SYMIG	42	-1232.1726	2704.3219	0.0012	1.0000
HKY	39	-1259.0094	2740.8543	0.0000	1.0000
GTR	43	-1247.6418	2740.9741	0.0000	1.0000
K2P	36	-1268.7976	2743.2895	0.0000	1.0000
SYM	40	-1260.1819	2748.9132	0.0000	1.0000
JC69G	36	-1277.9851	2761.6646	0.0000	1.0000
F81G	39	-1271.0001	2764.8359	0.0000	1.0000
JC69I	36	-1280.2130	2766.1203	0.0000	1.0000
JC69IG	37	-1277.8873	2767.1827	0.0000	1.0000
F81I	39	-1273.1663	2769.1682	0.0000	1.0000
F81IG	40	-1270.8852	2770.3197	0.0000	1.0000
JC69	35	-1303.9081	2807.7969	0.0000	1.0000
F81	38	-1296.5492	2810.2202	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/chr1_19426.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19426.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/chr1_19426.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19426.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/chr1_19426.phylip = 1 - 303;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_19426.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

