
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:53 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_28.phylip" (19 taxa, 387 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1461.5327	3012.5452	0.3991	0.3991
HKYI	40	-1461.7265	3012.9328	0.3288	0.7279
HKYIG	41	-1461.3303	3014.6432	0.1398	0.8677
GTRG	44	-1458.3728	3016.3246	0.0603	0.9281
GTRI	44	-1458.5443	3016.6675	0.0508	0.9789
GTRIG	45	-1458.1411	3018.4229	0.0211	1.0000
SYMI	41	-1473.0974	3038.1774	0.0000	1.0000
SYMG	41	-1473.2538	3038.4903	0.0000	1.0000
SYMIG	42	-1472.9041	3040.3083	0.0000	1.0000
K2PG	37	-1479.5580	3041.1733	0.0000	1.0000
K2PIG	38	-1479.2864	3043.0901	0.0000	1.0000
GTR	43	-1475.3016	3047.6353	0.0000	1.0000
K2PI	37	-1483.7540	3049.5653	0.0000	1.0000
HKY	39	-1483.6223	3054.2359	0.0000	1.0000
SYM	40	-1488.6082	3066.6962	0.0000	1.0000
F81G	39	-1492.2316	3071.4546	0.0000	1.0000
F81I	39	-1492.4407	3071.8727	0.0000	1.0000
F81IG	40	-1492.0413	3073.5624	0.0000	1.0000
K2P	36	-1500.0413	3079.6940	0.0000	1.0000
JC69G	36	-1513.5721	3106.7557	0.0000	1.0000
JC69IG	37	-1513.2929	3108.6430	0.0000	1.0000
F81	38	-1514.8287	3114.1747	0.0000	1.0000
JC69I	36	-1518.7478	3117.1071	0.0000	1.0000
JC69	35	-1533.9172	3145.0139	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1461.5327	3003.0654	0.3058	0.3058
HKYI	40	-1461.7265	3003.4531	0.2519	0.5578
HKYIG	41	-1461.3303	3004.6606	0.1378	0.6955
GTRG	44	-1458.3728	3004.7456	0.1320	0.8276
GTRI	44	-1458.5443	3005.0886	0.1112	0.9388
GTRIG	45	-1458.1411	3006.2822	0.0612	1.0000
SYMI	41	-1473.0974	3028.1948	0.0000	1.0000
SYMG	41	-1473.2538	3028.5077	0.0000	1.0000
SYMIG	42	-1472.9041	3029.8083	0.0000	1.0000
K2PG	37	-1479.5580	3033.1160	0.0000	1.0000
K2PIG	38	-1479.2864	3034.5729	0.0000	1.0000
GTR	43	-1475.3016	3036.6032	0.0000	1.0000
K2PI	37	-1483.7540	3041.5080	0.0000	1.0000
HKY	39	-1483.6223	3045.2445	0.0000	1.0000
SYM	40	-1488.6082	3057.2164	0.0000	1.0000
F81G	39	-1492.2316	3062.4632	0.0000	1.0000
F81I	39	-1492.4407	3062.8813	0.0000	1.0000
F81IG	40	-1492.0413	3064.0826	0.0000	1.0000
K2P	36	-1500.0413	3072.0826	0.0000	1.0000
JC69G	36	-1513.5721	3099.1442	0.0000	1.0000
JC69IG	37	-1513.2929	3100.5857	0.0000	1.0000
F81	38	-1514.8287	3105.6575	0.0000	1.0000
JC69I	36	-1518.7478	3109.4956	0.0000	1.0000
JC69	35	-1533.9172	3137.8344	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1461.5327	3161.4024	0.5301	0.5301
HKYI	40	-1461.7265	3161.7900	0.4367	0.9668
HKYIG	41	-1461.3303	3166.9560	0.0330	0.9998
GTRG	44	-1458.3728	3178.9163	0.0001	0.9999
GTRI	44	-1458.5443	3179.2592	0.0001	0.9999
K2PG	37	-1479.5580	3179.5777	0.0001	1.0000
GTRIG	45	-1458.1411	3184.4113	0.0000	1.0000
K2PIG	38	-1479.2864	3184.9930	0.0000	1.0000
K2PI	37	-1483.7540	3187.9698	0.0000	1.0000
SYMI	41	-1473.0974	3190.4903	0.0000	1.0000
SYMG	41	-1473.2538	3190.8031	0.0000	1.0000
SYMIG	42	-1472.9041	3196.0621	0.0000	1.0000
HKY	39	-1483.6223	3199.6231	0.0000	1.0000
GTR	43	-1475.3016	3206.8155	0.0000	1.0000
K2P	36	-1500.0413	3214.5859	0.0000	1.0000
SYM	40	-1488.6082	3215.5534	0.0000	1.0000
F81G	39	-1492.2316	3216.8418	0.0000	1.0000
F81I	39	-1492.4407	3217.2599	0.0000	1.0000
F81IG	40	-1492.0413	3222.4196	0.0000	1.0000
JC69G	36	-1513.5721	3241.6475	0.0000	1.0000
JC69IG	37	-1513.2929	3247.0474	0.0000	1.0000
JC69I	36	-1518.7478	3251.9989	0.0000	1.0000
F81	38	-1514.8287	3256.0776	0.0000	1.0000
JC69	35	-1533.9172	3276.3793	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_28.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_28.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_28.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_28.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_28.phylip = 1 - 387;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_28.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

