
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:56 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_21301.phylip" (19 taxa, 544 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: HKYG
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
HKYG	40	-1465.1330	3016.7870	0.1938	0.1938
HKYIG	41	-1464.0365	3016.9335	0.1801	0.3739
HKYI	40	-1465.2584	3017.0377	0.1710	0.5449
GTRG	44	-1460.5700	3017.0759	0.1677	0.7126
GTRIG	45	-1459.4224	3017.1580	0.1610	0.8736
GTRI	44	-1460.8528	3017.6415	0.1264	1.0000
K2PG	37	-1482.0957	3043.7488	0.0000	1.0000
SYMG	41	-1477.5275	3043.9155	0.0000	1.0000
K2PI	37	-1482.2226	3044.0026	0.0000	1.0000
K2PIG	38	-1481.1110	3044.0913	0.0000	1.0000
SYMIG	42	-1476.4923	3044.1942	0.0000	1.0000
SYMI	41	-1477.9219	3044.7043	0.0000	1.0000
F81G	39	-1497.9354	3080.0614	0.0000	1.0000
F81I	39	-1498.0515	3080.2935	0.0000	1.0000
F81IG	40	-1497.0367	3080.5943	0.0000	1.0000
GTR	43	-1494.7921	3083.1523	0.0000	1.0000
HKY	39	-1500.8045	3085.7995	0.0000	1.0000
JC69G	36	-1512.2783	3101.8109	0.0000	1.0000
JC69I	36	-1512.4001	3102.0546	0.0000	1.0000
JC69IG	37	-1511.4231	3102.4035	0.0000	1.0000
SYM	40	-1509.9904	3106.5016	0.0000	1.0000
K2P	36	-1517.0522	3111.3588	0.0000	1.0000
F81	38	-1532.4815	3146.8324	0.0000	1.0000
JC69	35	-1546.3151	3167.5908	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1459.4224	3008.8448	0.2513	0.2513
GTRG	44	-1460.5700	3009.1400	0.2168	0.4682
GTRI	44	-1460.8528	3009.7056	0.1634	0.6316
HKYIG	41	-1464.0365	3010.0729	0.1360	0.7676
HKYG	40	-1465.1330	3010.2661	0.1235	0.8911
HKYI	40	-1465.2584	3010.5169	0.1089	1.0000
SYMIG	42	-1476.4923	3036.9846	0.0000	1.0000
SYMG	41	-1477.5275	3037.0549	0.0000	1.0000
SYMI	41	-1477.9219	3037.8438	0.0000	1.0000
K2PG	37	-1482.0957	3038.1915	0.0000	1.0000
K2PIG	38	-1481.1110	3038.2220	0.0000	1.0000
K2PI	37	-1482.2226	3038.4453	0.0000	1.0000
F81G	39	-1497.9354	3073.8709	0.0000	1.0000
F81IG	40	-1497.0367	3074.0734	0.0000	1.0000
F81I	39	-1498.0515	3074.1031	0.0000	1.0000
GTR	43	-1494.7921	3075.5843	0.0000	1.0000
HKY	39	-1500.8045	3079.6090	0.0000	1.0000
JC69G	36	-1512.2783	3096.5565	0.0000	1.0000
JC69I	36	-1512.4001	3096.8001	0.0000	1.0000
JC69IG	37	-1511.4231	3096.8462	0.0000	1.0000
SYM	40	-1509.9904	3099.9807	0.0000	1.0000
K2P	36	-1517.0522	3106.1044	0.0000	1.0000
F81	38	-1532.4815	3140.9631	0.0000	1.0000
JC69	35	-1546.3151	3162.6302	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1465.1330	3182.2240	0.4970	0.4970
HKYI	40	-1465.2584	3182.4748	0.4384	0.9354
HKYIG	41	-1464.0365	3186.3299	0.0638	0.9992
K2PG	37	-1482.0957	3197.2526	0.0003	0.9994
K2PI	37	-1482.2226	3197.5064	0.0002	0.9997
GTRG	44	-1460.5700	3198.2938	0.0002	0.9998
GTRI	44	-1460.8528	3198.8594	0.0001	0.9999
K2PIG	38	-1481.1110	3201.5821	0.0000	1.0000
GTRIG	45	-1459.4224	3202.2975	0.0000	1.0000
SYMG	41	-1477.5275	3213.3118	0.0000	1.0000
SYMI	41	-1477.9219	3214.1007	0.0000	1.0000
SYMIG	42	-1476.4923	3217.5405	0.0000	1.0000
F81G	39	-1497.9354	3241.5299	0.0000	1.0000
F81I	39	-1498.0515	3241.7621	0.0000	1.0000
F81IG	40	-1497.0367	3246.0314	0.0000	1.0000
HKY	39	-1500.8045	3247.2680	0.0000	1.0000
JC69G	36	-1512.2783	3251.3187	0.0000	1.0000
JC69I	36	-1512.4001	3251.5623	0.0000	1.0000
JC69IG	37	-1511.4231	3255.9073	0.0000	1.0000
GTR	43	-1494.7921	3260.4391	0.0000	1.0000
K2P	36	-1517.0522	3260.8665	0.0000	1.0000
SYM	40	-1509.9904	3271.9387	0.0000	1.0000
F81	38	-1532.4815	3304.3232	0.0000	1.0000
JC69	35	-1546.3151	3313.0934	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/chr2_21301.phylip = 1 - 544;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21301.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21301.phylip = 1 - 544;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21301.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;


[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_21301.phylip = 1 - 544;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21301.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

