
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:31 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/chr6_3257.phylip" (19 taxa, 541 characters)

Minimum AIC  model: GTRG
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	-1581.8936	3250.3472	0.3242	0.3242
HKYI	40	-1582.2889	3251.1378	0.2183	0.5425
GTRG	44	-1577.7197	3251.4232	0.1893	0.7318
HKYIG	41	-1581.8501	3252.6021	0.1050	0.8368
GTRI	44	-1578.3418	3252.6675	0.1016	0.9385
GTRIG	45	-1577.6534	3253.6705	0.0615	1.0000
K2PG	37	-1597.6333	3274.8570	0.0000	1.0000
K2PI	37	-1597.9986	3275.5877	0.0000	1.0000
K2PIG	38	-1597.6023	3277.1089	0.0000	1.0000
SYMG	41	-1596.5634	3282.0287	0.0000	1.0000
SYMI	41	-1597.0292	3282.9601	0.0000	1.0000
SYMIG	42	-1596.5156	3284.2842	0.0000	1.0000
HKY	39	-1600.8913	3286.0101	0.0000	1.0000
GTR	43	-1596.9858	3287.5853	0.0000	1.0000
F81G	39	-1606.4104	3297.0484	0.0000	1.0000
F81I	39	-1606.8730	3297.9736	0.0000	1.0000
F81IG	40	-1606.3916	3299.3432	0.0000	1.0000
K2P	36	-1616.6684	3310.6226	0.0000	1.0000
SYM	40	-1614.5796	3315.7193	0.0000	1.0000
JC69G	36	-1619.6358	3316.5574	0.0000	1.0000
JC69I	36	-1620.0820	3317.4497	0.0000	1.0000
JC69IG	37	-1619.6184	3318.8273	0.0000	1.0000
F81	38	-1625.1871	3332.2786	0.0000	1.0000
JC69	35	-1638.6179	3352.2260	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1577.7197	3243.4393	0.2733	0.2733
HKYG	40	-1581.8936	3243.7872	0.2297	0.5030
HKYI	40	-1582.2889	3244.5778	0.1547	0.6576
GTRI	44	-1578.3418	3244.6837	0.1467	0.8043
GTRIG	45	-1577.6534	3245.3069	0.1074	0.9118
HKYIG	41	-1581.8501	3245.7003	0.0882	1.0000
K2PG	37	-1597.6333	3269.2665	0.0000	1.0000
K2PI	37	-1597.9986	3269.9973	0.0000	1.0000
K2PIG	38	-1597.6023	3271.2045	0.0000	1.0000
SYMG	41	-1596.5634	3275.1269	0.0000	1.0000
SYMI	41	-1597.0292	3276.0583	0.0000	1.0000
SYMIG	42	-1596.5156	3277.0312	0.0000	1.0000
HKY	39	-1600.8913	3279.7825	0.0000	1.0000
GTR	43	-1596.9858	3279.9716	0.0000	1.0000
F81G	39	-1606.4104	3290.8208	0.0000	1.0000
F81I	39	-1606.8730	3291.7461	0.0000	1.0000
F81IG	40	-1606.3916	3292.7832	0.0000	1.0000
K2P	36	-1616.6684	3305.3369	0.0000	1.0000
SYM	40	-1614.5796	3309.1593	0.0000	1.0000
JC69G	36	-1619.6358	3311.2717	0.0000	1.0000
JC69I	36	-1620.0820	3312.1640	0.0000	1.0000
JC69IG	37	-1619.6184	3313.2368	0.0000	1.0000
F81	38	-1625.1871	3326.3742	0.0000	1.0000
JC69	35	-1638.6179	3347.2359	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1581.8936	3415.5240	0.5807	0.5807
HKYI	40	-1582.2889	3416.3145	0.3911	0.9719
HKYIG	41	-1581.8501	3421.7305	0.0261	0.9979
K2PG	37	-1597.6333	3428.1231	0.0011	0.9990
K2PI	37	-1597.9986	3428.8538	0.0007	0.9997
GTRG	44	-1577.7197	3432.3497	0.0001	0.9999
GTRI	44	-1578.3418	3433.5941	0.0001	0.9999
K2PIG	38	-1597.6023	3434.3545	0.0000	1.0000
GTRIG	45	-1577.6534	3438.5107	0.0000	1.0000
HKY	39	-1600.8913	3447.2259	0.0000	1.0000
SYMG	41	-1596.5634	3451.1571	0.0000	1.0000
SYMI	41	-1597.0292	3452.0885	0.0000	1.0000
SYMIG	42	-1596.5156	3457.3548	0.0000	1.0000
F81G	39	-1606.4104	3458.2642	0.0000	1.0000
F81I	39	-1606.8730	3459.1894	0.0000	1.0000
K2P	36	-1616.6684	3459.9000	0.0000	1.0000
F81IG	40	-1606.3916	3464.5200	0.0000	1.0000
GTR	43	-1596.9858	3464.5886	0.0000	1.0000
JC69G	36	-1619.6358	3465.8348	0.0000	1.0000
JC69I	36	-1620.0820	3466.7271	0.0000	1.0000
JC69IG	37	-1619.6184	3472.0933	0.0000	1.0000
SYM	40	-1614.5796	3480.8960	0.0000	1.0000
F81	38	-1625.1871	3489.5242	0.0000	1.0000
JC69	35	-1638.6179	3497.5055	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/chr6_3257.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3257.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3257.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3257.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/chr6_3257.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3257.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

