
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:19 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_894.phylip" (19 taxa, 1085 characters)

Minimum AIC  model: GTRG
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	-3369.1765	6821.4947	0.3145	0.3145
GTRG	44	-3365.0375	6821.8827	0.2590	0.5735
HKYIG	41	-3368.4524	6822.2068	0.2203	0.7938
GTRIG	45	-3364.2497	6822.4841	0.1918	0.9855
HKYI	40	-3372.5963	6828.3344	0.0103	0.9958
GTRI	44	-3369.1585	6830.1246	0.0042	1.0000
SYMG	41	-3387.9633	6861.2286	0.0000	1.0000
SYMIG	42	-3387.2486	6861.9635	0.0000	1.0000
K2PG	37	-3395.2065	6867.0987	0.0000	1.0000
K2PIG	38	-3394.5583	6867.9502	0.0000	1.0000
SYMI	41	-3392.4594	6870.2207	0.0000	1.0000
K2PI	37	-3398.7953	6874.2764	0.0000	1.0000
F81G	39	-3407.3727	6895.7310	0.0000	1.0000
F81IG	40	-3406.7753	6896.6924	0.0000	1.0000
F81I	39	-3411.1940	6903.3736	0.0000	1.0000
GTR	43	-3413.2844	6916.2037	0.0000	1.0000
HKY	39	-3417.7208	6916.4272	0.0000	1.0000
JC69G	36	-3430.5093	6935.5606	0.0000	1.0000
JC69IG	37	-3429.9396	6936.5650	0.0000	1.0000
JC69I	36	-3434.3462	6943.2344	0.0000	1.0000
SYM	40	-3434.5543	6952.2504	0.0000	1.0000
K2P	36	-3441.9310	6958.4039	0.0000	1.0000
F81	38	-3451.3741	6981.5819	0.0000	1.0000
JC69	35	-3474.2164	7020.8352	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3365.0375	6818.0750	0.2955	0.2955
HKYG	40	-3369.1765	6818.3530	0.2572	0.5527
GTRIG	45	-3364.2497	6818.4995	0.2390	0.7916
HKYIG	41	-3368.4524	6818.9048	0.1951	0.9868
HKYI	40	-3372.5963	6825.1926	0.0084	0.9952
GTRI	44	-3369.1585	6826.3169	0.0048	1.0000
SYMG	41	-3387.9633	6857.9266	0.0000	1.0000
SYMIG	42	-3387.2486	6858.4971	0.0000	1.0000
K2PG	37	-3395.2065	6864.4129	0.0000	1.0000
K2PIG	38	-3394.5583	6865.1166	0.0000	1.0000
SYMI	41	-3392.4594	6866.9187	0.0000	1.0000
K2PI	37	-3398.7953	6871.5906	0.0000	1.0000
F81G	39	-3407.3727	6892.7454	0.0000	1.0000
F81IG	40	-3406.7753	6893.5506	0.0000	1.0000
F81I	39	-3411.1940	6900.3880	0.0000	1.0000
GTR	43	-3413.2844	6912.5688	0.0000	1.0000
HKY	39	-3417.7208	6913.4416	0.0000	1.0000
JC69G	36	-3430.5093	6933.0187	0.0000	1.0000
JC69IG	37	-3429.9396	6933.8792	0.0000	1.0000
JC69I	36	-3434.3462	6940.6924	0.0000	1.0000
SYM	40	-3434.5543	6949.1087	0.0000	1.0000
K2P	36	-3441.9310	6955.8619	0.0000	1.0000
F81	38	-3451.3741	6978.7482	0.0000	1.0000
JC69	35	-3474.2164	7018.4329	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3369.1765	7017.9264	0.9129	0.9129
HKYIG	41	-3368.4524	7023.4675	0.0572	0.9701
HKYI	40	-3372.5963	7024.7661	0.0299	0.9999
GTRG	44	-3365.0375	7037.6058	0.0000	1.0000
GTRIG	45	-3364.2497	7043.0196	0.0000	1.0000
GTRI	44	-3369.1585	7045.8477	0.0000	1.0000
K2PG	37	-3395.2065	7049.0183	0.0000	1.0000
K2PIG	38	-3394.5583	7054.7113	0.0000	1.0000
K2PI	37	-3398.7953	7056.1960	0.0000	1.0000
SYMG	41	-3387.9633	7062.4894	0.0000	1.0000
SYMIG	42	-3387.2486	7068.0492	0.0000	1.0000
SYMI	41	-3392.4594	7071.4815	0.0000	1.0000
F81G	39	-3407.3727	7087.3295	0.0000	1.0000
F81IG	40	-3406.7753	7093.1240	0.0000	1.0000
F81I	39	-3411.1940	7094.9721	0.0000	1.0000
HKY	39	-3417.7208	7108.0257	0.0000	1.0000
JC69G	36	-3430.5093	7112.6347	0.0000	1.0000
JC69IG	37	-3429.9396	7118.4846	0.0000	1.0000
JC69I	36	-3434.3462	7120.3084	0.0000	1.0000
GTR	43	-3413.2844	7127.1102	0.0000	1.0000
K2P	36	-3441.9310	7135.4780	0.0000	1.0000
SYM	40	-3434.5543	7148.6821	0.0000	1.0000
F81	38	-3451.3741	7168.3429	0.0000	1.0000
JC69	35	-3474.2164	7193.0596	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_894.phylip = 1 - 1085;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_894.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_894.phylip = 1 - 1085;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_894.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/chr4_894.phylip = 1 - 1085;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_894.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

