
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:02 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/chr2_4035.phylip" (19 taxa, 412 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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	-1334.1966	2767.1835	0.5137	0.5137
GTRI	44	-1335.0429	2768.8759	0.2204	0.7341
GTRIG	45	-1334.1847	2769.6808	0.1474	0.8815
HKYG	40	-1340.9972	2770.8355	0.0827	0.9642
HKYIG	41	-1340.9274	2773.1629	0.0258	0.9900
HKYI	40	-1343.1148	2775.0705	0.0100	1.0000
GTR	43	-1355.6339	2807.5503	0.0000	1.0000
K2PG	37	-1364.8982	2811.3152	0.0000	1.0000
K2PIG	38	-1364.8529	2813.6521	0.0000	1.0000
SYMG	41	-1361.2412	2813.7904	0.0000	1.0000
F81G	39	-1364.1545	2814.6961	0.0000	1.0000
K2PI	37	-1366.7696	2815.0579	0.0000	1.0000
HKY	39	-1364.6495	2815.6861	0.0000	1.0000
SYMI	41	-1362.4544	2816.2170	0.0000	1.0000
SYMIG	42	-1361.2308	2816.2502	0.0000	1.0000
F81I	39	-1368.4580	2823.3030	0.0000	1.0000
F81IG	40	-1367.7590	2824.3590	0.0000	1.0000
K2P	36	-1386.6653	2852.4346	0.0000	1.0000
SYM	40	-1381.8788	2852.5985	0.0000	1.0000
JC69G	36	-1390.4233	2859.9505	0.0000	1.0000
F81	38	-1388.2931	2860.5325	0.0000	1.0000
JC69I	36	-1395.0055	2869.1150	0.0000	1.0000
JC69IG	37	-1394.1396	2869.7978	0.0000	1.0000
JC69	35	-1414.1733	2905.0487	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1334.1966	2756.3933	0.5281	0.5281
GTRI	44	-1335.0429	2758.0857	0.2266	0.7547
GTRIG	45	-1334.1847	2758.3693	0.1966	0.9514
HKYG	40	-1340.9972	2761.9945	0.0321	0.9835
HKYIG	41	-1340.9274	2763.8548	0.0127	0.9961
HKYI	40	-1343.1148	2766.2295	0.0039	1.0000
GTR	43	-1355.6339	2797.2677	0.0000	1.0000
K2PG	37	-1364.8982	2803.7965	0.0000	1.0000
SYMG	41	-1361.2412	2804.4823	0.0000	1.0000
K2PIG	38	-1364.8529	2805.7057	0.0000	1.0000
F81G	39	-1364.1545	2806.3090	0.0000	1.0000
SYMIG	42	-1361.2308	2806.4616	0.0000	1.0000
SYMI	41	-1362.4544	2806.9089	0.0000	1.0000
HKY	39	-1364.6495	2807.2990	0.0000	1.0000
K2PI	37	-1366.7696	2807.5392	0.0000	1.0000
F81I	39	-1368.4580	2814.9159	0.0000	1.0000
F81IG	40	-1367.7590	2815.5180	0.0000	1.0000
SYM	40	-1381.8788	2843.7575	0.0000	1.0000
K2P	36	-1386.6653	2845.3306	0.0000	1.0000
F81	38	-1388.2931	2852.5861	0.0000	1.0000
JC69G	36	-1390.4233	2852.8465	0.0000	1.0000
JC69I	36	-1395.0055	2862.0110	0.0000	1.0000
JC69IG	37	-1394.1396	2862.2791	0.0000	1.0000
JC69	35	-1414.1733	2898.3465	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1340.9972	2922.8354	0.8467	0.8467
HKYI	40	-1343.1148	2927.0705	0.1019	0.9486
HKYIG	41	-1340.9274	2928.7167	0.0447	0.9934
GTRG	44	-1334.1966	2933.3183	0.0045	0.9979
GTRI	44	-1335.0429	2935.0107	0.0019	0.9998
GTRIG	45	-1334.1847	2939.3154	0.0002	1.0000
K2PG	37	-1364.8982	2952.5743	0.0000	1.0000
K2PI	37	-1366.7696	2956.3171	0.0000	1.0000
K2PIG	38	-1364.8529	2958.5046	0.0000	1.0000
F81G	39	-1364.1545	2963.1289	0.0000	1.0000
HKY	39	-1364.6495	2964.1189	0.0000	1.0000
SYMG	41	-1361.2412	2969.3443	0.0000	1.0000
GTR	43	-1355.6339	2970.1717	0.0000	1.0000
F81I	39	-1368.4580	2971.7358	0.0000	1.0000
SYMI	41	-1362.4544	2971.7709	0.0000	1.0000
SYMIG	42	-1361.2308	2975.3446	0.0000	1.0000
F81IG	40	-1367.7590	2976.3589	0.0000	1.0000
K2P	36	-1386.6653	2990.0874	0.0000	1.0000
JC69G	36	-1390.4233	2997.6034	0.0000	1.0000
SYM	40	-1381.8788	3004.5985	0.0000	1.0000
F81	38	-1388.2931	3005.3850	0.0000	1.0000
JC69I	36	-1395.0055	3006.7679	0.0000	1.0000
JC69IG	37	-1394.1396	3011.0570	0.0000	1.0000
JC69	35	-1414.1733	3039.0824	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/chr2_4035.phylip = 1 - 412;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4035.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/chr2_4035.phylip = 1 - 412;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4035.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4035.phylip = 1 - 412;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4035.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

