
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:09 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/chr13_696.phylip" (19 taxa, 865 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	-3270.2199	6633.2690	0.4670	0.4670
GTRI	44	-3270.6509	6634.1311	0.3034	0.7704
GTRIG	45	-3269.8921	6634.8392	0.2130	0.9834
HKYG	40	-3278.7228	6641.4262	0.0079	0.9913
HKYI	40	-3278.9927	6641.9660	0.0060	0.9973
HKYIG	41	-3278.6930	6643.5707	0.0027	1.0000
SYMG	41	-3295.5551	6677.2950	0.0000	1.0000
SYMI	41	-3295.5975	6677.3798	0.0000	1.0000
SYMIG	42	-3295.1970	6678.7881	0.0000	1.0000
K2PG	37	-3301.1400	6679.6802	0.0000	1.0000
K2PI	37	-3301.7903	6680.9809	0.0000	1.0000
K2PIG	38	-3300.7476	6681.0835	0.0000	1.0000
GTR	43	-3306.6442	6703.8975	0.0000	1.0000
HKY	39	-3315.4536	6712.6889	0.0000	1.0000
SYM	40	-3332.0096	6747.9999	0.0000	1.0000
K2P	36	-3338.0765	6751.3703	0.0000	1.0000
F81G	39	-3374.6038	6830.9894	0.0000	1.0000
F81I	39	-3374.6515	6831.0847	0.0000	1.0000
F81IG	40	-3374.1172	6832.2150	0.0000	1.0000
JC69I	36	-3391.6642	6858.5459	0.0000	1.0000
JC69G	36	-3391.7546	6858.7266	0.0000	1.0000
JC69IG	37	-3391.2253	6859.8508	0.0000	1.0000
F81	38	-3407.7327	6895.0538	0.0000	1.0000
JC69	35	-3423.0296	6919.0991	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3270.2199	6628.4397	0.4579	0.4579
GTRI	44	-3270.6509	6629.3019	0.2975	0.7554
GTRIG	45	-3269.8921	6629.7842	0.2338	0.9891
HKYG	40	-3278.7228	6637.4456	0.0051	0.9942
HKYI	40	-3278.9927	6637.9854	0.0039	0.9981
HKYIG	41	-3278.6930	6639.3860	0.0019	1.0000
SYMG	41	-3295.5551	6673.1103	0.0000	1.0000
SYMI	41	-3295.5975	6673.1951	0.0000	1.0000
SYMIG	42	-3295.1970	6674.3940	0.0000	1.0000
K2PG	37	-3301.1400	6676.2800	0.0000	1.0000
K2PIG	38	-3300.7476	6677.4952	0.0000	1.0000
K2PI	37	-3301.7903	6677.5806	0.0000	1.0000
GTR	43	-3306.6442	6699.2885	0.0000	1.0000
HKY	39	-3315.4536	6708.9071	0.0000	1.0000
SYM	40	-3332.0096	6744.0193	0.0000	1.0000
K2P	36	-3338.0765	6748.1529	0.0000	1.0000
F81G	39	-3374.6038	6827.2076	0.0000	1.0000
F81I	39	-3374.6515	6827.3029	0.0000	1.0000
F81IG	40	-3374.1172	6828.2344	0.0000	1.0000
JC69I	36	-3391.6642	6855.3285	0.0000	1.0000
JC69G	36	-3391.7546	6855.5092	0.0000	1.0000
JC69IG	37	-3391.2253	6856.4506	0.0000	1.0000
F81	38	-3407.7327	6891.4654	0.0000	1.0000
JC69	35	-3423.0296	6916.0593	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3278.7228	6827.9548	0.5526	0.5526
HKYI	40	-3278.9927	6828.4946	0.4219	0.9745
HKYIG	41	-3278.6930	6834.6579	0.0194	0.9938
GTRG	44	-3270.2199	6837.9998	0.0036	0.9975
GTRI	44	-3270.6509	6838.8620	0.0024	0.9998
GTRIG	45	-3269.8921	6844.1070	0.0002	1.0000
K2PG	37	-3301.1400	6852.5010	0.0000	1.0000
K2PI	37	-3301.7903	6853.8016	0.0000	1.0000
K2PIG	38	-3300.7476	6858.4789	0.0000	1.0000
SYMG	41	-3295.5551	6868.3822	0.0000	1.0000
SYMI	41	-3295.5975	6868.4670	0.0000	1.0000
SYMIG	42	-3295.1970	6874.4286	0.0000	1.0000
HKY	39	-3315.4536	6894.6536	0.0000	1.0000
GTR	43	-3306.6442	6904.0858	0.0000	1.0000
K2P	36	-3338.0765	6919.6112	0.0000	1.0000
SYM	40	-3332.0096	6934.5285	0.0000	1.0000
F81G	39	-3374.6038	7012.9541	0.0000	1.0000
F81I	39	-3374.6515	7013.0494	0.0000	1.0000
F81IG	40	-3374.1172	7018.7436	0.0000	1.0000
JC69I	36	-3391.6642	7026.7867	0.0000	1.0000
JC69G	36	-3391.7546	7026.9675	0.0000	1.0000
JC69IG	37	-3391.2253	7032.6716	0.0000	1.0000
F81	38	-3407.7327	7072.4491	0.0000	1.0000
JC69	35	-3423.0296	7082.7548	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/chr13_696.phylip = 1 - 865;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_696.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/chr13_696.phylip = 1 - 865;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_696.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/chr13_696.phylip = 1 - 865;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_696.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

