
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:11 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/chr11_1600.phylip" (19 taxa, 443 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1413.9389	2925.8275	0.5043	0.5043
GTRI	44	-1414.3481	2926.6459	0.3350	0.8393
GTRIG	45	-1413.8823	2928.1927	0.1546	0.9939
HKYG	40	-1423.9818	2936.1229	0.0029	0.9968
HKYI	40	-1424.7217	2937.6027	0.0014	0.9982
HKYIG	41	-1423.8961	2938.3807	0.0009	0.9991
SYMG	41	-1424.9546	2940.4977	0.0003	0.9995
SYMI	41	-1425.5917	2941.7719	0.0002	0.9996
K2PG	37	-1430.6402	2942.2237	0.0001	0.9998
SYMIG	42	-1424.8375	2942.7051	0.0001	0.9999
K2PI	37	-1431.4565	2943.8561	0.0001	1.0000
K2PIG	38	-1430.4947	2944.3260	0.0000	1.0000
GTR	43	-1443.9102	2983.3041	0.0000	1.0000
HKY	39	-1453.5745	2992.8910	0.0000	1.0000
SYM	40	-1455.0627	2998.2845	0.0000	1.0000
K2P	36	-1461.0006	3000.5627	0.0000	1.0000
F81G	39	-1461.7026	3009.1472	0.0000	1.0000
F81I	39	-1462.1573	3010.0566	0.0000	1.0000
F81IG	40	-1461.7023	3011.5638	0.0000	1.0000
JC69G	36	-1466.8726	3012.3068	0.0000	1.0000
JC69I	36	-1467.5715	3013.7046	0.0000	1.0000
JC69IG	37	-1466.9520	3014.8471	0.0000	1.0000
F81	38	-1490.3278	3063.9922	0.0000	1.0000
JC69	35	-1496.1345	3068.4605	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1413.9389	2915.8778	0.4857	0.4857
GTRI	44	-1414.3481	2916.6962	0.3226	0.8084
GTRIG	45	-1413.8823	2917.7645	0.1891	0.9975
HKYG	40	-1423.9818	2927.9637	0.0012	0.9986
HKYI	40	-1424.7217	2929.4435	0.0006	0.9992
HKYIG	41	-1423.8961	2929.7921	0.0005	0.9996
SYMG	41	-1424.9546	2931.9091	0.0002	0.9998
SYMI	41	-1425.5917	2933.1834	0.0001	0.9999
SYMIG	42	-1424.8375	2933.6751	0.0001	0.9999
K2PG	37	-1430.6402	2935.2805	0.0000	1.0000
K2PI	37	-1431.4565	2936.9129	0.0000	1.0000
K2PIG	38	-1430.4947	2936.9893	0.0000	1.0000
GTR	43	-1443.9102	2973.8204	0.0000	1.0000
HKY	39	-1453.5745	2985.1490	0.0000	1.0000
SYM	40	-1455.0627	2990.1253	0.0000	1.0000
K2P	36	-1461.0006	2994.0011	0.0000	1.0000
F81G	39	-1461.7026	3001.4053	0.0000	1.0000
F81I	39	-1462.1573	3002.3147	0.0000	1.0000
F81IG	40	-1461.7023	3003.4046	0.0000	1.0000
JC69G	36	-1466.8726	3005.7452	0.0000	1.0000
JC69I	36	-1467.5715	3007.1431	0.0000	1.0000
JC69IG	37	-1466.9520	3007.9039	0.0000	1.0000
F81	38	-1490.3278	3056.6555	0.0000	1.0000
JC69	35	-1496.1345	3062.2689	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1430.6402	3086.7425	0.6083	0.6083
K2PI	37	-1431.4565	3088.3750	0.2689	0.8772
HKYG	40	-1423.9818	3091.7065	0.0508	0.9280
K2PIG	38	-1430.4947	3092.5450	0.0334	0.9615
HKYI	40	-1424.7217	3093.1863	0.0243	0.9857
GTRG	44	-1413.9389	3095.9949	0.0060	0.9917
GTRI	44	-1414.3481	3096.8133	0.0040	0.9956
HKYIG	41	-1423.8961	3097.6285	0.0026	0.9983
SYMG	41	-1424.9546	3099.7455	0.0009	0.9992
SYMI	41	-1425.5917	3101.0198	0.0005	0.9997
GTRIG	45	-1413.8823	3101.9752	0.0003	1.0000
SYMIG	42	-1424.8375	3105.6050	0.0000	1.0000
K2P	36	-1461.0006	3141.3697	0.0000	1.0000
HKY	39	-1453.5745	3144.7982	0.0000	1.0000
GTR	43	-1443.9102	3149.8439	0.0000	1.0000
JC69G	36	-1466.8726	3153.1137	0.0000	1.0000
SYM	40	-1455.0627	3153.8681	0.0000	1.0000
JC69I	36	-1467.5715	3154.5116	0.0000	1.0000
JC69IG	37	-1466.9520	3159.3660	0.0000	1.0000
F81G	39	-1461.7026	3161.0545	0.0000	1.0000
F81I	39	-1462.1573	3161.9639	0.0000	1.0000
F81IG	40	-1461.7023	3167.1474	0.0000	1.0000
JC69	35	-1496.1345	3205.5438	0.0000	1.0000
F81	38	-1490.3278	3212.2112	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/chr11_1600.phylip = 1 - 443;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1600.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/chr11_1600.phylip = 1 - 443;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1600.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1600.phylip = 1 - 443;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1600.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

