
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:34 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/chr3_9700.phylip" (19 taxa, 451 characters)

Minimum AIC  model: GTRG
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	-1441.8567	2981.4671	0.7217	0.7217
GTRIG	45	-1441.5790	2983.3801	0.2773	0.9990
GTRI	44	-1448.4756	2994.7048	0.0010	1.0000
HKYG	40	-1457.2868	3002.5736	0.0000	1.0000
HKYIG	41	-1456.1860	3002.7926	0.0000	1.0000
HKYI	40	-1461.6401	3011.2802	0.0000	1.0000
SYMG	41	-1476.3552	3043.1309	0.0000	1.0000
SYMIG	42	-1476.5197	3045.8924	0.0000	1.0000
GTR	43	-1479.4927	3054.2827	0.0000	1.0000
K2PG	37	-1487.8080	3056.4246	0.0000	1.0000
SYMI	41	-1483.2117	3056.8440	0.0000	1.0000
K2PIG	38	-1486.8313	3056.8568	0.0000	1.0000
K2PI	37	-1492.8628	3066.5342	0.0000	1.0000
HKY	39	-1497.3544	3080.3000	0.0000	1.0000
F81G	39	-1499.1727	3083.9367	0.0000	1.0000
F81IG	40	-1498.6204	3085.2407	0.0000	1.0000
F81I	39	-1503.3208	3092.2328	0.0000	1.0000
SYM	40	-1510.1253	3108.2505	0.0000	1.0000
JC69G	36	-1523.5167	3125.4683	0.0000	1.0000
JC69IG	37	-1522.9456	3126.6999	0.0000	1.0000
K2P	36	-1524.3393	3127.1133	0.0000	1.0000
JC69I	36	-1527.6403	3133.7155	0.0000	1.0000
F81	38	-1532.4857	3148.1657	0.0000	1.0000
JC69	35	-1556.9566	3189.9855	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1441.8567	2971.7134	0.6725	0.6725
GTRIG	45	-1441.5790	2973.1579	0.3266	0.9991
GTRI	44	-1448.4756	2984.9511	0.0009	1.0000
HKYIG	41	-1456.1860	2994.3720	0.0000	1.0000
HKYG	40	-1457.2868	2994.5736	0.0000	1.0000
HKYI	40	-1461.6401	3003.2802	0.0000	1.0000
SYMG	41	-1476.3552	3034.7104	0.0000	1.0000
SYMIG	42	-1476.5197	3037.0395	0.0000	1.0000
GTR	43	-1479.4927	3044.9854	0.0000	1.0000
SYMI	41	-1483.2117	3048.4235	0.0000	1.0000
K2PG	37	-1487.8080	3049.6159	0.0000	1.0000
K2PIG	38	-1486.8313	3049.6626	0.0000	1.0000
K2PI	37	-1492.8628	3059.7255	0.0000	1.0000
HKY	39	-1497.3544	3072.7087	0.0000	1.0000
F81G	39	-1499.1727	3076.3454	0.0000	1.0000
F81IG	40	-1498.6204	3077.2407	0.0000	1.0000
F81I	39	-1503.3208	3084.6416	0.0000	1.0000
SYM	40	-1510.1253	3100.2505	0.0000	1.0000
JC69G	36	-1523.5167	3119.0335	0.0000	1.0000
JC69IG	37	-1522.9456	3119.8912	0.0000	1.0000
K2P	36	-1524.3393	3120.6785	0.0000	1.0000
JC69I	36	-1527.6403	3127.2807	0.0000	1.0000
F81	38	-1532.4857	3140.9715	0.0000	1.0000
JC69	35	-1556.9566	3183.9132	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1441.8567	3152.6180	0.9007	0.9007
GTRIG	45	-1441.5790	3158.1739	0.0560	0.9567
HKYG	40	-1457.2868	3159.0323	0.0365	0.9932
HKYIG	41	-1456.1860	3162.9422	0.0052	0.9983
GTRI	44	-1448.4756	3165.8557	0.0012	0.9995
HKYI	40	-1461.6401	3167.7389	0.0005	1.0000
K2PG	37	-1487.8080	3201.7402	0.0000	1.0000
SYMG	41	-1476.3552	3203.2806	0.0000	1.0000
K2PIG	38	-1486.8313	3205.8984	0.0000	1.0000
SYMIG	42	-1476.5197	3209.7211	0.0000	1.0000
K2PI	37	-1492.8628	3211.8498	0.0000	1.0000
SYMI	41	-1483.2117	3216.9937	0.0000	1.0000
GTR	43	-1479.4927	3221.7785	0.0000	1.0000
HKY	39	-1497.3544	3233.0559	0.0000	1.0000
F81G	39	-1499.1727	3236.6927	0.0000	1.0000
F81IG	40	-1498.6204	3241.6994	0.0000	1.0000
F81I	39	-1503.3208	3244.9888	0.0000	1.0000
SYM	40	-1510.1253	3264.7092	0.0000	1.0000
JC69G	36	-1523.5167	3267.0463	0.0000	1.0000
K2P	36	-1524.3393	3268.6913	0.0000	1.0000
JC69IG	37	-1522.9456	3272.0155	0.0000	1.0000
JC69I	36	-1527.6403	3275.2935	0.0000	1.0000
F81	38	-1532.4857	3297.2072	0.0000	1.0000
JC69	35	-1556.9566	3327.8146	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/chr3_9700.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9700.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/chr3_9700.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9700.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/chr3_9700.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9700.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

