
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:23 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_34708.phylip" (19 taxa, 659 characters)

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


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	-2770.9962	5636.4418	0.5290	0.5290
GTRIG	45	-2769.9927	5636.7390	0.4560	0.9850
HKYIG	41	-2778.0200	5643.6218	0.0146	0.9996
GTRI	44	-2778.7153	5651.8802	0.0002	0.9998
HKYG	40	-2783.4715	5652.2504	0.0002	1.0000
SYMG	41	-2785.8804	5659.3426	0.0000	1.0000
SYMIG	42	-2784.8019	5659.4675	0.0000	1.0000
HKYI	40	-2791.2932	5667.8939	0.0000	1.0000
K2PG	37	-2797.7546	5674.0374	0.0000	1.0000
K2PIG	38	-2796.8598	5674.5003	0.0000	1.0000
SYMI	41	-2793.5703	5674.7225	0.0000	1.0000
K2PI	37	-2805.8672	5690.2625	0.0000	1.0000
F81G	39	-2869.6925	5822.4255	0.0000	1.0000
F81IG	40	-2869.0102	5823.3279	0.0000	1.0000
F81I	39	-2877.3759	5837.7922	0.0000	1.0000
GTR	43	-2873.7366	5839.6261	0.0000	1.0000
HKY	39	-2880.6536	5844.3475	0.0000	1.0000
SYM	40	-2883.9861	5853.2797	0.0000	1.0000
JC69G	36	-2889.2146	5854.7122	0.0000	1.0000
JC69IG	37	-2888.6122	5855.7526	0.0000	1.0000
K2P	36	-2892.9350	5862.1529	0.0000	1.0000
JC69I	36	-2896.3288	5868.9406	0.0000	1.0000
F81	38	-2956.2009	5993.1824	0.0000	1.0000
JC69	35	-2973.6510	6021.3469	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2769.9927	5629.9853	0.4963	0.4963
GTRG	44	-2770.9962	5629.9923	0.4945	0.9908
HKYIG	41	-2778.0200	5638.0399	0.0088	0.9997
GTRI	44	-2778.7153	5645.4307	0.0002	0.9999
HKYG	40	-2783.4715	5646.9430	0.0001	1.0000
SYMIG	42	-2784.8019	5653.6038	0.0000	1.0000
SYMG	41	-2785.8804	5653.7607	0.0000	1.0000
HKYI	40	-2791.2932	5662.5865	0.0000	1.0000
SYMI	41	-2793.5703	5669.1406	0.0000	1.0000
K2PG	37	-2797.7546	5669.5092	0.0000	1.0000
K2PIG	38	-2796.8598	5669.7197	0.0000	1.0000
K2PI	37	-2805.8672	5685.7343	0.0000	1.0000
F81G	39	-2869.6925	5817.3851	0.0000	1.0000
F81IG	40	-2869.0102	5818.0204	0.0000	1.0000
F81I	39	-2877.3759	5832.7518	0.0000	1.0000
GTR	43	-2873.7366	5833.4732	0.0000	1.0000
HKY	39	-2880.6536	5839.3071	0.0000	1.0000
SYM	40	-2883.9861	5847.9723	0.0000	1.0000
JC69G	36	-2889.2146	5850.4293	0.0000	1.0000
JC69IG	37	-2888.6122	5851.2245	0.0000	1.0000
K2P	36	-2892.9350	5857.8699	0.0000	1.0000
JC69I	36	-2896.3288	5864.6576	0.0000	1.0000
F81	38	-2956.2009	5988.4018	0.0000	1.0000
JC69	35	-2973.6510	6017.3020	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-2778.0200	5822.1596	0.8436	0.8436
HKYG	40	-2783.4715	5826.5719	0.0929	0.9365
GTRG	44	-2770.9962	5827.5842	0.0560	0.9925
GTRIG	45	-2769.9927	5832.0679	0.0060	0.9985
K2PG	37	-2797.7546	5835.6660	0.0010	0.9995
SYMG	41	-2785.8804	5837.8804	0.0003	0.9998
K2PIG	38	-2796.8598	5840.3672	0.0001	0.9999
SYMIG	42	-2784.8019	5842.2142	0.0000	0.9999
HKYI	40	-2791.2932	5842.2154	0.0000	1.0000
GTRI	44	-2778.7153	5843.0225	0.0000	1.0000
K2PI	37	-2805.8672	5851.8911	0.0000	1.0000
SYMI	41	-2793.5703	5853.2603	0.0000	1.0000
F81G	39	-2869.6925	5992.5233	0.0000	1.0000
F81IG	40	-2869.0102	5997.6494	0.0000	1.0000
F81I	39	-2877.3759	6007.8900	0.0000	1.0000
JC69G	36	-2889.2146	6012.0953	0.0000	1.0000
HKY	39	-2880.6536	6014.4454	0.0000	1.0000
JC69IG	37	-2888.6122	6017.3812	0.0000	1.0000
K2P	36	-2892.9350	6019.5360	0.0000	1.0000
JC69I	36	-2896.3288	6026.3236	0.0000	1.0000
GTR	43	-2873.7366	6026.5744	0.0000	1.0000
SYM	40	-2883.9861	6027.6012	0.0000	1.0000
F81	38	-2956.2009	6159.0493	0.0000	1.0000
JC69	35	-2973.6510	6174.4773	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_34708.phylip = 1 - 659;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34708.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_34708.phylip = 1 - 659;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34708.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34708.phylip = 1 - 659;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34708.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

