
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:54 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_27261.phylip" (19 taxa, 462 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	-1381.8758	2861.2479	0.5801	0.5801
GTRIG	45	-1381.5971	2863.1461	0.2245	0.8046
GTRI	44	-1382.9641	2863.4246	0.1954	1.0000
HKYG	40	-1399.2538	2886.2985	0.0000	1.0000
HKYIG	41	-1398.8915	2887.9830	0.0000	1.0000
HKYI	40	-1400.1716	2888.1341	0.0000	1.0000
SYMG	41	-1406.6478	2903.4956	0.0000	1.0000
SYMI	41	-1407.2528	2904.7056	0.0000	1.0000
SYMIG	42	-1406.3294	2905.2793	0.0000	1.0000
GTR	43	-1408.8393	2912.7312	0.0000	1.0000
K2PG	37	-1417.9470	2916.5262	0.0000	1.0000
K2PIG	38	-1417.5226	2918.0524	0.0000	1.0000
K2PI	37	-1418.7783	2918.1887	0.0000	1.0000
HKY	39	-1424.3773	2934.1479	0.0000	1.0000
SYM	40	-1432.4335	2952.6580	0.0000	1.0000
K2P	36	-1443.3196	2964.9074	0.0000	1.0000
F81G	39	-1443.5727	2972.5388	0.0000	1.0000
F81I	39	-1444.2967	2973.9867	0.0000	1.0000
F81IG	40	-1443.2392	2974.2694	0.0000	1.0000
JC69G	36	-1458.3619	2994.9920	0.0000	1.0000
JC69I	36	-1459.0673	2996.4029	0.0000	1.0000
JC69IG	37	-1457.9822	2996.5966	0.0000	1.0000
F81	38	-1467.3997	3017.8065	0.0000	1.0000
JC69	35	-1482.4654	3040.8463	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1381.8758	2851.7515	0.5486	0.5486
GTRIG	45	-1381.5971	2853.1942	0.2667	0.8152
GTRI	44	-1382.9641	2853.9282	0.1848	1.0000
HKYG	40	-1399.2538	2878.5075	0.0000	1.0000
HKYIG	41	-1398.8915	2879.7830	0.0000	1.0000
HKYI	40	-1400.1716	2880.3431	0.0000	1.0000
SYMG	41	-1406.6478	2895.2956	0.0000	1.0000
SYMI	41	-1407.2528	2896.5056	0.0000	1.0000
SYMIG	42	-1406.3294	2896.6588	0.0000	1.0000
GTR	43	-1408.8393	2903.6785	0.0000	1.0000
K2PG	37	-1417.9470	2909.8941	0.0000	1.0000
K2PIG	38	-1417.5226	2911.0453	0.0000	1.0000
K2PI	37	-1418.7783	2911.5567	0.0000	1.0000
HKY	39	-1424.3773	2926.7545	0.0000	1.0000
SYM	40	-1432.4335	2944.8671	0.0000	1.0000
K2P	36	-1443.3196	2958.6391	0.0000	1.0000
F81G	39	-1443.5727	2965.1454	0.0000	1.0000
F81IG	40	-1443.2392	2966.4784	0.0000	1.0000
F81I	39	-1444.2967	2966.5933	0.0000	1.0000
JC69G	36	-1458.3619	2988.7238	0.0000	1.0000
JC69IG	37	-1457.9822	2989.9645	0.0000	1.0000
JC69I	36	-1459.0673	2990.1346	0.0000	1.0000
F81	38	-1467.3997	3010.7994	0.0000	1.0000
JC69	35	-1482.4654	3034.9308	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1381.8758	3033.7164	0.7107	0.7107
GTRI	44	-1382.9641	3035.8930	0.2393	0.9500
GTRIG	45	-1381.5971	3039.2946	0.0437	0.9937
HKYG	40	-1399.2538	3043.9301	0.0043	0.9980
HKYI	40	-1400.1716	3045.7657	0.0017	0.9997
HKYIG	41	-1398.8915	3049.3412	0.0003	1.0000
K2PG	37	-1417.9470	3062.9100	0.0000	1.0000
K2PI	37	-1418.7783	3064.5726	0.0000	1.0000
SYMG	41	-1406.6478	3064.8538	0.0000	1.0000
SYMI	41	-1407.2528	3066.0637	0.0000	1.0000
K2PIG	38	-1417.5226	3068.1967	0.0000	1.0000
SYMIG	42	-1406.3294	3070.3525	0.0000	1.0000
GTR	43	-1408.8393	3081.5078	0.0000	1.0000
HKY	39	-1424.3773	3088.0416	0.0000	1.0000
K2P	36	-1443.3196	3107.5195	0.0000	1.0000
SYM	40	-1432.4335	3110.2897	0.0000	1.0000
F81G	39	-1443.5727	3126.4325	0.0000	1.0000
F81I	39	-1444.2967	3127.8804	0.0000	1.0000
F81IG	40	-1443.2392	3131.9010	0.0000	1.0000
JC69G	36	-1458.3619	3137.6041	0.0000	1.0000
JC69I	36	-1459.0673	3139.0150	0.0000	1.0000
JC69IG	37	-1457.9822	3142.9804	0.0000	1.0000
F81	38	-1467.3997	3167.9509	0.0000	1.0000
JC69	35	-1482.4654	3179.6755	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/chr2_27261.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27261.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/chr2_27261.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27261.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/chr2_27261.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27261.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

