
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/chr2_24881.phylip" (19 taxa, 390 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	-1590.7966	3270.9915	0.6311	0.6311
HKYIG	41	-1590.8010	3273.4985	0.1802	0.8112
GTRG	44	-1587.6974	3274.8730	0.0906	0.9019
HKYI	40	-1593.0673	3275.5328	0.0652	0.9670
GTRIG	45	-1587.7014	3277.4377	0.0251	0.9922
GTRI	44	-1590.1457	3279.7697	0.0078	1.0000
K2PG	37	-1605.4539	3292.8964	0.0000	1.0000
K2PIG	38	-1605.4570	3295.3584	0.0000	1.0000
K2PI	37	-1607.8658	3297.7203	0.0000	1.0000
SYMG	41	-1604.6159	3301.1284	0.0000	1.0000
HKY	39	-1607.3158	3301.5458	0.0000	1.0000
SYMIG	42	-1604.6177	3303.6446	0.0000	1.0000
GTR	43	-1604.2418	3305.4200	0.0000	1.0000
SYMI	41	-1607.0780	3306.0525	0.0000	1.0000
K2P	36	-1620.6755	3320.8978	0.0000	1.0000
SYM	40	-1619.7063	3328.8110	0.0000	1.0000
F81G	39	-1645.9705	3378.8553	0.0000	1.0000
F81IG	40	-1645.9692	3381.3367	0.0000	1.0000
F81I	39	-1648.1301	3383.1745	0.0000	1.0000
JC69G	36	-1658.4224	3396.3916	0.0000	1.0000
JC69IG	37	-1658.4221	3398.8328	0.0000	1.0000
JC69I	36	-1660.6399	3400.8264	0.0000	1.0000
F81	38	-1660.1949	3404.8343	0.0000	1.0000
JC69	35	-1672.3893	3421.8973	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1590.7966	3261.5932	0.4855	0.4855
GTRG	44	-1587.6974	3263.3948	0.1972	0.6827
HKYIG	41	-1590.8010	3263.6019	0.1778	0.8606
GTRIG	45	-1587.7014	3265.4028	0.0723	0.9328
HKYI	40	-1593.0673	3266.1345	0.0501	0.9829
GTRI	44	-1590.1457	3268.2914	0.0170	1.0000
K2PG	37	-1605.4539	3284.9077	0.0000	1.0000
K2PIG	38	-1605.4570	3286.9139	0.0000	1.0000
K2PI	37	-1607.8658	3289.7316	0.0000	1.0000
SYMG	41	-1604.6159	3291.2319	0.0000	1.0000
HKY	39	-1607.3158	3292.6315	0.0000	1.0000
SYMIG	42	-1604.6177	3293.2353	0.0000	1.0000
GTR	43	-1604.2418	3294.4836	0.0000	1.0000
SYMI	41	-1607.0780	3296.1559	0.0000	1.0000
K2P	36	-1620.6755	3313.3510	0.0000	1.0000
SYM	40	-1619.7063	3319.4127	0.0000	1.0000
F81G	39	-1645.9705	3369.9410	0.0000	1.0000
F81IG	40	-1645.9692	3371.9384	0.0000	1.0000
F81I	39	-1648.1301	3374.2602	0.0000	1.0000
JC69G	36	-1658.4224	3388.8448	0.0000	1.0000
JC69IG	37	-1658.4221	3390.8441	0.0000	1.0000
JC69I	36	-1660.6399	3393.2797	0.0000	1.0000
F81	38	-1660.1949	3396.3898	0.0000	1.0000
JC69	35	-1672.3893	3414.7787	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1590.7966	3420.2391	0.8638	0.8638
HKYI	40	-1593.0673	3424.7804	0.0892	0.9530
HKYIG	41	-1590.8010	3426.2140	0.0436	0.9966
K2PG	37	-1605.4539	3431.6552	0.0029	0.9995
K2PI	37	-1607.8658	3436.4791	0.0003	0.9997
K2PIG	38	-1605.4570	3437.6275	0.0001	0.9999
GTRG	44	-1587.6974	3437.9052	0.0001	1.0000
GTRI	44	-1590.1457	3442.8019	0.0000	1.0000
GTRIG	45	-1587.7014	3443.8794	0.0000	1.0000
HKY	39	-1607.3158	3447.3112	0.0000	1.0000
SYMG	41	-1604.6159	3453.8439	0.0000	1.0000
K2P	36	-1620.6755	3456.1323	0.0000	1.0000
SYMI	41	-1607.0780	3458.7680	0.0000	1.0000
SYMIG	42	-1604.6177	3459.8135	0.0000	1.0000
GTR	43	-1604.2418	3465.0279	0.0000	1.0000
SYM	40	-1619.7063	3478.0586	0.0000	1.0000
F81G	39	-1645.9705	3524.6207	0.0000	1.0000
F81I	39	-1648.1301	3528.9399	0.0000	1.0000
F81IG	40	-1645.9692	3530.5843	0.0000	1.0000
JC69G	36	-1658.4224	3531.6261	0.0000	1.0000
JC69I	36	-1660.6399	3536.0610	0.0000	1.0000
JC69IG	37	-1658.4221	3537.5916	0.0000	1.0000
F81	38	-1660.1949	3547.1034	0.0000	1.0000
JC69	35	-1672.3893	3553.5938	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/chr2_24881.phylip = 1 - 390;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24881.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/chr2_24881.phylip = 1 - 390;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24881.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/chr2_24881.phylip = 1 - 390;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24881.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

