
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:52 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_12041.phylip" (19 taxa, 821 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: SYMG


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
GTRIG	45	-3275.8273	6646.9966	0.5593	0.5593
GTRG	44	-3277.6078	6648.3187	0.2887	0.8480
SYMG	41	-3282.0694	6650.5599	0.0942	0.9422
SYMIG	42	-3281.4459	6651.5344	0.0578	1.0000
HKYIG	41	-3291.7360	6669.8930	0.0000	1.0000
HKYG	40	-3294.1028	6672.4107	0.0000	1.0000
K2PG	37	-3299.0661	6675.7236	0.0000	1.0000
K2PIG	38	-3298.4115	6676.6132	0.0000	1.0000
SYMI	41	-3295.9505	6678.3220	0.0000	1.0000
GTRI	44	-3293.4649	6680.0329	0.0000	1.0000
K2PI	37	-3311.8301	6701.2516	0.0000	1.0000
HKYI	40	-3309.6192	6703.4435	0.0000	1.0000
F81G	39	-3343.9673	6769.9294	0.0000	1.0000
F81IG	40	-3343.4590	6771.1232	0.0000	1.0000
JC69G	36	-3348.8696	6773.1371	0.0000	1.0000
JC69IG	37	-3348.3736	6774.3386	0.0000	1.0000
JC69I	36	-3359.5442	6794.4864	0.0000	1.0000
F81I	39	-3356.2993	6794.5935	0.0000	1.0000
SYM	40	-3361.7246	6807.6544	0.0000	1.0000
GTR	43	-3358.5882	6808.0464	0.0000	1.0000
HKY	39	-3375.6122	6833.2193	0.0000	1.0000
K2P	36	-3380.1004	6835.5988	0.0000	1.0000
F81	38	-3419.2857	6918.3617	0.0000	1.0000
JC69	35	-3423.3104	6919.8310	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3275.8273	6641.6546	0.6107	0.6107
GTRG	44	-3277.6078	6643.2156	0.2798	0.8906
SYMG	41	-3282.0694	6646.1388	0.0649	0.9555
SYMIG	42	-3281.4459	6646.8917	0.0445	1.0000
HKYIG	41	-3291.7360	6665.4720	0.0000	1.0000
HKYG	40	-3294.1028	6668.2055	0.0000	1.0000
K2PG	37	-3299.0661	6672.1323	0.0000	1.0000
K2PIG	38	-3298.4115	6672.8229	0.0000	1.0000
SYMI	41	-3295.9505	6673.9009	0.0000	1.0000
GTRI	44	-3293.4649	6674.9298	0.0000	1.0000
K2PI	37	-3311.8301	6697.6603	0.0000	1.0000
HKYI	40	-3309.6192	6699.2384	0.0000	1.0000
F81G	39	-3343.9673	6765.9345	0.0000	1.0000
F81IG	40	-3343.4590	6766.9181	0.0000	1.0000
JC69G	36	-3348.8696	6769.7391	0.0000	1.0000
JC69IG	37	-3348.3736	6770.7473	0.0000	1.0000
F81I	39	-3356.2993	6790.5986	0.0000	1.0000
JC69I	36	-3359.5442	6791.0884	0.0000	1.0000
GTR	43	-3358.5882	6803.1764	0.0000	1.0000
SYM	40	-3361.7246	6803.4492	0.0000	1.0000
HKY	39	-3375.6122	6829.2244	0.0000	1.0000
K2P	36	-3380.1004	6832.2008	0.0000	1.0000
F81	38	-3419.2857	6914.5714	0.0000	1.0000
JC69	35	-3423.3104	6916.6208	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-3282.0694	6839.2703	0.9094	0.9094
SYMIG	42	-3281.4459	6844.7337	0.0592	0.9686
K2PG	37	-3299.0661	6846.4216	0.0255	0.9940
GTRG	44	-3277.6078	6850.4786	0.0033	0.9974
K2PIG	38	-3298.4115	6851.8228	0.0017	0.9991
GTRIG	45	-3275.8273	6853.6282	0.0007	0.9998
HKYG	40	-3294.1028	6856.6265	0.0002	0.9999
HKYIG	41	-3291.7360	6858.6034	0.0001	1.0000
SYMI	41	-3295.9505	6867.0324	0.0000	1.0000
K2PI	37	-3311.8301	6871.9496	0.0000	1.0000
GTRI	44	-3293.4649	6882.1928	0.0000	1.0000
HKYI	40	-3309.6192	6887.6593	0.0000	1.0000
JC69G	36	-3348.8696	6939.3180	0.0000	1.0000
JC69IG	37	-3348.3736	6945.0366	0.0000	1.0000
F81G	39	-3343.9673	6949.6449	0.0000	1.0000
F81IG	40	-3343.4590	6955.3390	0.0000	1.0000
JC69I	36	-3359.5442	6960.6672	0.0000	1.0000
F81I	39	-3356.2993	6974.3090	0.0000	1.0000
SYM	40	-3361.7246	6991.8702	0.0000	1.0000
K2P	36	-3380.1004	7001.7797	0.0000	1.0000
GTR	43	-3358.5882	7005.7289	0.0000	1.0000
HKY	39	-3375.6122	7012.9348	0.0000	1.0000
JC69	35	-3423.3104	7081.4891	0.0000	1.0000
F81	38	-3419.2857	7093.5713	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.phylip = 1 - 821;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_12041.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=Fixed(Equal);
END;


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End of Output

