
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:10 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/chr3_5766.phylip" (19 taxa, 433 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1282.6907	2663.5875	0.5459	0.5459
GTRI	44	-1283.4965	2665.1991	0.2439	0.7898
GTRIG	45	-1282.6094	2665.9165	0.1704	0.9601
HKYG	40	-1290.9559	2670.2791	0.0192	0.9793
HKYI	40	-1291.3522	2671.0717	0.0129	0.9923
HKYIG	41	-1290.9359	2672.6800	0.0058	0.9981
SYMG	41	-1293.1740	2677.1561	0.0006	0.9987
K2PG	37	-1298.4707	2678.0603	0.0004	0.9991
SYMI	41	-1293.7602	2678.3286	0.0003	0.9994
K2PI	37	-1298.8897	2678.8983	0.0003	0.9997
SYMIG	42	-1293.1154	2679.4923	0.0002	0.9999
K2PIG	38	-1298.4353	2680.3935	0.0001	1.0000
GTR	43	-1299.3067	2694.3408	0.0000	1.0000
HKY	39	-1307.3718	2700.6826	0.0000	1.0000
SYM	40	-1309.0598	2706.4870	0.0000	1.0000
K2P	36	-1314.8727	2708.4727	0.0000	1.0000
F81G	39	-1324.2058	2734.3505	0.0000	1.0000
F81I	39	-1324.7060	2735.3510	0.0000	1.0000
F81IG	40	-1324.1605	2736.6883	0.0000	1.0000
JC69G	36	-1329.9492	2738.6257	0.0000	1.0000
JC69I	36	-1330.4623	2739.6520	0.0000	1.0000
JC69IG	37	-1329.8967	2740.9124	0.0000	1.0000
F81	38	-1340.2833	2764.0894	0.0000	1.0000
JC69	35	-1346.0794	2768.5065	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1282.6907	2653.3813	0.5331	0.5331
GTRI	44	-1283.4965	2654.9929	0.2381	0.7712
GTRIG	45	-1282.6094	2655.2189	0.2127	0.9839
HKYG	40	-1290.9559	2661.9118	0.0075	0.9914
HKYI	40	-1291.3522	2662.7044	0.0050	0.9964
HKYIG	41	-1290.9359	2663.8718	0.0028	0.9992
SYMG	41	-1293.1740	2668.3480	0.0003	0.9995
SYMI	41	-1293.7602	2669.5204	0.0002	0.9997
SYMIG	42	-1293.1154	2670.2307	0.0001	0.9998
K2PG	37	-1298.4707	2670.9414	0.0001	0.9999
K2PI	37	-1298.8897	2671.7794	0.0001	1.0000
K2PIG	38	-1298.4353	2672.8706	0.0000	1.0000
GTR	43	-1299.3067	2684.6133	0.0000	1.0000
HKY	39	-1307.3718	2692.7437	0.0000	1.0000
SYM	40	-1309.0598	2698.1196	0.0000	1.0000
K2P	36	-1314.8727	2701.7454	0.0000	1.0000
F81G	39	-1324.2058	2726.4116	0.0000	1.0000
F81I	39	-1324.7060	2727.4121	0.0000	1.0000
F81IG	40	-1324.1605	2728.3209	0.0000	1.0000
JC69G	36	-1329.9492	2731.8984	0.0000	1.0000
JC69I	36	-1330.4623	2732.9247	0.0000	1.0000
JC69IG	37	-1329.8967	2733.7934	0.0000	1.0000
F81	38	-1340.2833	2756.5666	0.0000	1.0000
JC69	35	-1346.0794	2762.1589	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1298.4707	2821.5587	0.4840	0.4840
K2PI	37	-1298.8897	2822.3967	0.3183	0.8023
HKYG	40	-1290.9559	2824.7413	0.0986	0.9009
HKYI	40	-1291.3522	2825.5339	0.0663	0.9672
K2PIG	38	-1298.4353	2827.5587	0.0241	0.9913
HKYIG	41	-1290.9359	2830.7721	0.0048	0.9961
GTRG	44	-1282.6907	2832.4938	0.0020	0.9982
GTRI	44	-1283.4965	2834.1054	0.0009	0.9991
SYMG	41	-1293.1740	2835.2482	0.0005	0.9996
SYMI	41	-1293.7602	2836.4207	0.0003	0.9999
GTRIG	45	-1282.6094	2838.4021	0.0001	1.0000
SYMIG	42	-1293.1154	2841.2017	0.0000	1.0000
K2P	36	-1314.8727	2848.2920	0.0000	1.0000
HKY	39	-1307.3718	2851.5025	0.0000	1.0000
GTR	43	-1299.3067	2859.6550	0.0000	1.0000
SYM	40	-1309.0598	2860.9491	0.0000	1.0000
JC69G	36	-1329.9492	2878.4450	0.0000	1.0000
JC69I	36	-1330.4623	2879.4712	0.0000	1.0000
JC69IG	37	-1329.8967	2884.4107	0.0000	1.0000
F81G	39	-1324.2058	2885.1703	0.0000	1.0000
F81I	39	-1324.7060	2886.1708	0.0000	1.0000
F81IG	40	-1324.1605	2891.1504	0.0000	1.0000
JC69	35	-1346.0794	2904.6347	0.0000	1.0000
F81	38	-1340.2833	2911.2546	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/chr3_5766.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5766.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/chr3_5766.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5766.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5766.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5766.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

