
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:06 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/chr19_2740.phylip" (19 taxa, 826 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	-2782.0942	5657.2588	0.6464	0.6464
GTRIG	45	-2781.5979	5658.5034	0.3469	0.9933
GTRI	44	-2786.6682	5666.4068	0.0067	1.0000
HKYG	40	-2801.8925	5687.9633	0.0000	1.0000
SYMG	41	-2801.8769	5690.1466	0.0000	1.0000
SYMIG	42	-2801.3246	5691.2622	0.0000	1.0000
HKYIG	41	-2802.8664	5692.1256	0.0000	1.0000
HKYI	40	-2807.0034	5698.1851	0.0000	1.0000
SYMI	41	-2805.9853	5698.3635	0.0000	1.0000
K2PG	37	-2823.0476	5723.6637	0.0000	1.0000
K2PIG	38	-2824.0544	5727.8750	0.0000	1.0000
K2PI	37	-2828.0918	5733.7522	0.0000	1.0000
F81G	39	-2840.7915	5763.5526	0.0000	1.0000
F81IG	40	-2839.9625	5764.1033	0.0000	1.0000
F81I	39	-2844.1172	5770.2038	0.0000	1.0000
JC69G	36	-2866.9604	5809.2973	0.0000	1.0000
JC69IG	37	-2866.1532	5809.8749	0.0000	1.0000
JC69I	36	-2870.2337	5815.8438	0.0000	1.0000
GTR	43	-2862.6523	5816.1435	0.0000	1.0000
SYM	40	-2880.9085	5845.9953	0.0000	1.0000
HKY	39	-2882.7097	5847.3888	0.0000	1.0000
K2P	36	-2903.1852	5881.7469	0.0000	1.0000
F81	38	-2919.3049	5918.3759	0.0000	1.0000
JC69	35	-2943.1669	5959.5238	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2782.0942	5652.1884	0.6193	0.6193
GTRIG	45	-2781.5979	5653.1957	0.3743	0.9936
GTRI	44	-2786.6682	5661.3364	0.0064	1.0000
HKYG	40	-2801.8925	5683.7850	0.0000	1.0000
SYMG	41	-2801.8769	5685.7537	0.0000	1.0000
SYMIG	42	-2801.3246	5686.6491	0.0000	1.0000
HKYIG	41	-2802.8664	5687.7328	0.0000	1.0000
SYMI	41	-2805.9853	5693.9707	0.0000	1.0000
HKYI	40	-2807.0034	5694.0068	0.0000	1.0000
K2PG	37	-2823.0476	5720.0951	0.0000	1.0000
K2PIG	38	-2824.0544	5724.1088	0.0000	1.0000
K2PI	37	-2828.0918	5730.1836	0.0000	1.0000
F81G	39	-2840.7915	5759.5831	0.0000	1.0000
F81IG	40	-2839.9625	5759.9250	0.0000	1.0000
F81I	39	-2844.1172	5766.2343	0.0000	1.0000
JC69G	36	-2866.9604	5805.9209	0.0000	1.0000
JC69IG	37	-2866.1532	5806.3064	0.0000	1.0000
GTR	43	-2862.6523	5811.3047	0.0000	1.0000
JC69I	36	-2870.2337	5812.4673	0.0000	1.0000
SYM	40	-2880.9085	5841.8170	0.0000	1.0000
HKY	39	-2882.7097	5843.4193	0.0000	1.0000
K2P	36	-2903.1852	5878.3704	0.0000	1.0000
F81	38	-2919.3049	5914.6097	0.0000	1.0000
JC69	35	-2943.1669	5956.3339	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-2782.0942	5859.7185	0.9352	0.9352
GTRIG	45	-2781.5979	5865.4425	0.0535	0.9887
GTRI	44	-2786.6682	5868.8666	0.0096	0.9983
HKYG	40	-2801.8925	5872.4488	0.0016	0.9999
SYMG	41	-2801.8769	5879.1341	0.0001	1.0000
HKYIG	41	-2802.8664	5881.1131	0.0000	1.0000
HKYI	40	-2807.0034	5882.6706	0.0000	1.0000
SYMIG	42	-2801.3246	5884.7461	0.0000	1.0000
SYMI	41	-2805.9853	5887.3511	0.0000	1.0000
K2PG	37	-2823.0476	5894.6091	0.0000	1.0000
K2PIG	38	-2824.0544	5903.3394	0.0000	1.0000
K2PI	37	-2828.0918	5904.6976	0.0000	1.0000
F81G	39	-2840.7915	5943.5303	0.0000	1.0000
F81IG	40	-2839.9625	5948.5888	0.0000	1.0000
F81I	39	-2844.1172	5950.1815	0.0000	1.0000
JC69G	36	-2866.9604	5975.7183	0.0000	1.0000
JC69IG	37	-2866.1532	5980.8204	0.0000	1.0000
JC69I	36	-2870.2337	5982.2648	0.0000	1.0000
GTR	43	-2862.6523	6014.1182	0.0000	1.0000
HKY	39	-2882.7097	6027.3665	0.0000	1.0000
SYM	40	-2880.9085	6030.4808	0.0000	1.0000
K2P	36	-2903.1852	6048.1679	0.0000	1.0000
F81	38	-2919.3049	6093.8403	0.0000	1.0000
JC69	35	-2943.1669	6121.4147	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/chr19_2740.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2740.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/chr19_2740.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2740.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/chr19_2740.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2740.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

