
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:31 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_30635.phylip" (19 taxa, 989 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-3675.0197	7442.2344	0.5078	0.5078
GTRIG	45	-3673.9544	7442.2991	0.4916	0.9994
GTRI	44	-3681.7062	7455.6074	0.0006	1.0000
HKYIG	41	-3695.9629	7477.5626	0.0000	1.0000
HKYG	40	-3697.3153	7478.0906	0.0000	1.0000
HKYI	40	-3701.7480	7486.9559	0.0000	1.0000
SYMG	41	-3714.3161	7514.2689	0.0000	1.0000
SYMIG	42	-3713.9794	7515.7770	0.0000	1.0000
SYMI	41	-3721.0226	7527.6819	0.0000	1.0000
K2PG	37	-3730.5902	7538.1373	0.0000	1.0000
K2PIG	38	-3730.5271	7540.1743	0.0000	1.0000
K2PI	37	-3735.6611	7548.2791	0.0000	1.0000
F81G	39	-3765.8904	7613.0684	0.0000	1.0000
F81IG	40	-3765.3925	7614.2450	0.0000	1.0000
F81I	39	-3770.4368	7622.1612	0.0000	1.0000
JC69G	36	-3791.6599	7658.1182	0.0000	1.0000
JC69IG	37	-3791.5132	7659.9833	0.0000	1.0000
JC69I	36	-3796.6857	7668.1697	0.0000	1.0000
GTR	43	-3809.9557	7709.9157	0.0000	1.0000
HKY	39	-3831.2210	7743.7297	0.0000	1.0000
SYM	40	-3855.6973	7794.8546	0.0000	1.0000
K2P	36	-3866.1851	7807.1685	0.0000	1.0000
F81	38	-3900.9274	7880.9748	0.0000	1.0000
JC69	35	-3927.7369	7928.1181	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3673.9544	7437.9089	0.5160	0.5160
GTRG	44	-3675.0197	7438.0394	0.4834	0.9994
GTRI	44	-3681.7062	7451.4125	0.0006	1.0000
HKYIG	41	-3695.9629	7473.9258	0.0000	1.0000
HKYG	40	-3697.3153	7474.6306	0.0000	1.0000
HKYI	40	-3701.7480	7483.4959	0.0000	1.0000
SYMG	41	-3714.3161	7510.6322	0.0000	1.0000
SYMIG	42	-3713.9794	7511.9588	0.0000	1.0000
SYMI	41	-3721.0226	7524.0451	0.0000	1.0000
K2PG	37	-3730.5902	7535.1804	0.0000	1.0000
K2PIG	38	-3730.5271	7537.0543	0.0000	1.0000
K2PI	37	-3735.6611	7545.3222	0.0000	1.0000
F81G	39	-3765.8904	7609.7807	0.0000	1.0000
F81IG	40	-3765.3925	7610.7851	0.0000	1.0000
F81I	39	-3770.4368	7618.8735	0.0000	1.0000
JC69G	36	-3791.6599	7655.3199	0.0000	1.0000
JC69IG	37	-3791.5132	7657.0264	0.0000	1.0000
JC69I	36	-3796.6857	7665.3714	0.0000	1.0000
GTR	43	-3809.9557	7705.9114	0.0000	1.0000
HKY	39	-3831.2210	7740.4421	0.0000	1.0000
SYM	40	-3855.6973	7791.3947	0.0000	1.0000
K2P	36	-3866.1851	7804.3702	0.0000	1.0000
F81	38	-3900.9274	7877.8548	0.0000	1.0000
JC69	35	-3927.7369	7925.4739	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3675.0197	7653.4940	0.9143	0.9143
GTRIG	45	-3673.9544	7658.2601	0.0844	0.9986
GTRI	44	-3681.7062	7666.8670	0.0011	0.9998
HKYG	40	-3697.3153	7670.4984	0.0002	1.0000
HKYIG	41	-3695.9629	7674.6903	0.0000	1.0000
HKYI	40	-3701.7480	7679.3637	0.0000	1.0000
SYMG	41	-3714.3161	7711.3966	0.0000	1.0000
K2PG	37	-3730.5902	7716.3581	0.0000	1.0000
SYMIG	42	-3713.9794	7717.6200	0.0000	1.0000
K2PIG	38	-3730.5271	7723.1287	0.0000	1.0000
SYMI	41	-3721.0226	7724.8096	0.0000	1.0000
K2PI	37	-3735.6611	7726.4999	0.0000	1.0000
F81G	39	-3765.8904	7800.7518	0.0000	1.0000
F81IG	40	-3765.3925	7806.6529	0.0000	1.0000
F81I	39	-3770.4368	7809.8446	0.0000	1.0000
JC69G	36	-3791.6599	7831.6009	0.0000	1.0000
JC69IG	37	-3791.5132	7838.2041	0.0000	1.0000
JC69I	36	-3796.6857	7841.6524	0.0000	1.0000
GTR	43	-3809.9557	7916.4693	0.0000	1.0000
HKY	39	-3831.2210	7931.4131	0.0000	1.0000
K2P	36	-3866.1851	7980.6512	0.0000	1.0000
SYM	40	-3855.6973	7987.2625	0.0000	1.0000
F81	38	-3900.9274	8063.9292	0.0000	1.0000
JC69	35	-3927.7369	8096.8582	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30635.phylip = 1 - 989;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30635.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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_30635.phylip = 1 - 989;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30635.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30635.phylip = 1 - 989;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30635.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;


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End of Output

