
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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_24775.phylip" (19 taxa, 374 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1289.4198	2668.6894	0.4106	0.4106
HKYI	40	-1289.4633	2668.7764	0.3931	0.8037
HKYIG	41	-1289.4195	2671.2124	0.1163	0.9199
GTRI	44	-1287.0154	2674.0673	0.0279	0.9478
GTRG	44	-1287.0861	2674.2087	0.0260	0.9738
K2PG	37	-1297.0547	2676.4785	0.0084	0.9822
K2PI	37	-1297.1013	2676.5717	0.0080	0.9902
GTRIG	45	-1287.1361	2676.8942	0.0068	0.9970
K2PIG	38	-1297.0544	2678.9566	0.0024	0.9994
SYMI	41	-1295.4053	2683.1840	0.0003	0.9997
SYMG	41	-1295.5077	2683.3889	0.0003	0.9999
SYMIG	42	-1295.5668	2686.0461	0.0001	1.0000
HKY	39	-1304.8562	2697.0536	0.0000	1.0000
GTR	43	-1301.8186	2701.1040	0.0000	1.0000
K2P	36	-1312.7158	2705.3366	0.0000	1.0000
SYM	40	-1310.5832	2711.0163	0.0000	1.0000
F81I	39	-1326.3746	2740.0906	0.0000	1.0000
F81G	39	-1326.4364	2740.2141	0.0000	1.0000
F81IG	40	-1326.4942	2742.8382	0.0000	1.0000
JC69I	36	-1332.5754	2745.0557	0.0000	1.0000
JC69G	36	-1332.6119	2745.1289	0.0000	1.0000
JC69IG	37	-1332.6707	2747.7104	0.0000	1.0000
F81	38	-1341.0358	2766.9194	0.0000	1.0000
JC69	35	-1347.4650	2772.3856	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1289.4198	2658.8396	0.3561	0.3561
HKYI	40	-1289.4633	2658.9266	0.3410	0.6971
HKYIG	41	-1289.4195	2660.8389	0.1311	0.8282
GTRI	44	-1287.0154	2662.0308	0.0722	0.9004
GTRG	44	-1287.0861	2662.1723	0.0673	0.9677
GTRIG	45	-1287.1361	2664.2722	0.0235	0.9912
K2PG	37	-1297.0547	2668.1095	0.0035	0.9947
K2PI	37	-1297.1013	2668.2026	0.0033	0.9980
K2PIG	38	-1297.0544	2670.1089	0.0013	0.9993
SYMI	41	-1295.4053	2672.8105	0.0003	0.9996
SYMG	41	-1295.5077	2673.0154	0.0003	0.9999
SYMIG	42	-1295.5668	2675.1337	0.0001	1.0000
HKY	39	-1304.8562	2687.7123	0.0000	1.0000
GTR	43	-1301.8186	2689.6373	0.0000	1.0000
K2P	36	-1312.7158	2697.4316	0.0000	1.0000
SYM	40	-1310.5832	2701.1664	0.0000	1.0000
F81I	39	-1326.3746	2730.7493	0.0000	1.0000
F81G	39	-1326.4364	2730.8728	0.0000	1.0000
F81IG	40	-1326.4942	2732.9883	0.0000	1.0000
JC69I	36	-1332.5754	2737.1507	0.0000	1.0000
JC69G	36	-1332.6119	2737.2238	0.0000	1.0000
JC69IG	37	-1332.6707	2739.3414	0.0000	1.0000
F81	38	-1341.0358	2758.0716	0.0000	1.0000
JC69	35	-1347.4650	2764.9300	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1297.0547	2813.3069	0.3874	0.3874
K2PI	37	-1297.1013	2813.4001	0.3698	0.7572
HKYG	40	-1289.4198	2815.8098	0.1108	0.8681
HKYI	40	-1289.4633	2815.8968	0.1061	0.9742
K2PIG	38	-1297.0544	2819.2306	0.0200	0.9942
HKYIG	41	-1289.4195	2821.7334	0.0057	1.0000
SYMI	41	-1295.4053	2833.7050	0.0000	1.0000
SYMG	41	-1295.5077	2833.9099	0.0000	1.0000
GTRI	44	-1287.0154	2834.6981	0.0000	1.0000
GTRG	44	-1287.0861	2834.8395	0.0000	1.0000
K2P	36	-1312.7158	2838.7048	0.0000	1.0000
SYMIG	42	-1295.5668	2839.9524	0.0000	1.0000
HKY	39	-1304.8562	2840.7583	0.0000	1.0000
GTRIG	45	-1287.1361	2840.8637	0.0000	1.0000
SYM	40	-1310.5832	2858.1367	0.0000	1.0000
GTR	43	-1301.8186	2858.3803	0.0000	1.0000
JC69I	36	-1332.5754	2878.4239	0.0000	1.0000
JC69G	36	-1332.6119	2878.4970	0.0000	1.0000
F81I	39	-1326.3746	2883.7952	0.0000	1.0000
F81G	39	-1326.4364	2883.9187	0.0000	1.0000
JC69IG	37	-1332.6707	2884.5388	0.0000	1.0000
F81IG	40	-1326.4942	2889.9586	0.0000	1.0000
JC69	35	-1347.4650	2902.2789	0.0000	1.0000
F81	38	-1341.0358	2907.1933	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.phylip = 1 - 374;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.phylip = 1 - 374;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.phylip = 1 - 374;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_24775.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

