
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:38 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/chr4_7263.phylip" (19 taxa, 403 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1317.8541	2734.7696	0.7030	0.7030
GTRI	44	-1318.7478	2736.5571	0.2876	0.9907
HKYG	40	-1327.8820	2744.8247	0.0046	0.9953
HKYIG	41	-1327.2673	2746.0747	0.0025	0.9977
HKYI	40	-1328.5935	2746.2478	0.0023	1.0000
GTRIG	45	-1328.1572	2757.9109	0.0000	1.0000
SYMG	41	-1340.7660	2773.0722	0.0000	1.0000
GTR	43	-1347.9665	2792.4734	0.0000	1.0000
HKY	39	-1354.2747	2795.1443	0.0000	1.0000
K2PG	37	-1357.3066	2796.3174	0.0000	1.0000
SYMIG	42	-1351.1551	2796.3435	0.0000	1.0000
SYMI	41	-1352.9988	2797.5377	0.0000	1.0000
K2PI	37	-1359.1082	2799.9206	0.0000	1.0000
K2PIG	38	-1366.2861	2816.7150	0.0000	1.0000
SYM	40	-1371.1562	2831.3731	0.0000	1.0000
K2P	36	-1385.3848	2850.0482	0.0000	1.0000
F81G	39	-1393.5789	2873.7528	0.0000	1.0000
F81IG	40	-1393.3827	2875.8262	0.0000	1.0000
F81I	39	-1394.9007	2876.3964	0.0000	1.0000
F81	38	-1418.0104	2920.1636	0.0000	1.0000
JC69G	36	-1429.6502	2938.5790	0.0000	1.0000
JC69IG	37	-1429.3998	2940.5037	0.0000	1.0000
JC69I	36	-1431.2314	2941.7415	0.0000	1.0000
JC69	35	-1453.8709	2984.6083	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1317.8541	2723.7082	0.7070	0.7070
GTRI	44	-1318.7478	2725.4957	0.2893	0.9963
HKYG	40	-1327.8820	2735.7639	0.0017	0.9980
HKYIG	41	-1327.2673	2736.5345	0.0012	0.9992
HKYI	40	-1328.5935	2737.1871	0.0008	1.0000
GTRIG	45	-1328.1572	2746.3143	0.0000	1.0000
SYMG	41	-1340.7660	2763.5321	0.0000	1.0000
GTR	43	-1347.9665	2781.9330	0.0000	1.0000
SYMIG	42	-1351.1551	2786.3101	0.0000	1.0000
HKY	39	-1354.2747	2786.5493	0.0000	1.0000
SYMI	41	-1352.9988	2787.9975	0.0000	1.0000
K2PG	37	-1357.3066	2788.6133	0.0000	1.0000
K2PI	37	-1359.1082	2792.2165	0.0000	1.0000
K2PIG	38	-1366.2861	2808.5721	0.0000	1.0000
SYM	40	-1371.1562	2822.3124	0.0000	1.0000
K2P	36	-1385.3848	2842.7695	0.0000	1.0000
F81G	39	-1393.5789	2865.1578	0.0000	1.0000
F81IG	40	-1393.3827	2866.7654	0.0000	1.0000
F81I	39	-1394.9007	2867.8014	0.0000	1.0000
F81	38	-1418.0104	2912.0207	0.0000	1.0000
JC69G	36	-1429.6502	2931.3004	0.0000	1.0000
JC69IG	37	-1429.3998	2932.7996	0.0000	1.0000
JC69I	36	-1431.2314	2934.4629	0.0000	1.0000
JC69	35	-1453.8709	2977.7418	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1327.8820	2895.7214	0.5620	0.5620
HKYI	40	-1328.5935	2897.1445	0.2758	0.8378
GTRG	44	-1317.8541	2899.6614	0.0784	0.9162
HKYIG	41	-1327.2673	2900.4909	0.0518	0.9679
GTRI	44	-1318.7478	2901.4489	0.0321	1.0000
GTRIG	45	-1328.1572	2926.2664	0.0000	1.0000
SYMG	41	-1340.7660	2927.4885	0.0000	1.0000
K2PG	37	-1357.3066	2936.5740	0.0000	1.0000
K2PI	37	-1359.1082	2940.1772	0.0000	1.0000
HKY	39	-1354.2747	2942.5078	0.0000	1.0000
SYMI	41	-1352.9988	2951.9539	0.0000	1.0000
GTR	43	-1347.9665	2953.8873	0.0000	1.0000
SYMIG	42	-1351.1551	2954.2655	0.0000	1.0000
K2PIG	38	-1366.2861	2960.5317	0.0000	1.0000
SYM	40	-1371.1562	2982.2698	0.0000	1.0000
K2P	36	-1385.3848	2986.7313	0.0000	1.0000
F81G	39	-1393.5789	3021.1163	0.0000	1.0000
F81I	39	-1394.9007	3023.7599	0.0000	1.0000
F81IG	40	-1393.3827	3026.7228	0.0000	1.0000
F81	38	-1418.0104	3063.9803	0.0000	1.0000
JC69G	36	-1429.6502	3075.2621	0.0000	1.0000
JC69I	36	-1431.2314	3078.4246	0.0000	1.0000
JC69IG	37	-1429.3998	3080.7603	0.0000	1.0000
JC69	35	-1453.8709	3117.7046	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/chr4_7263.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7263.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/chr4_7263.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7263.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7263.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7263.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

