
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:34 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/chr9_5218.phylip" (19 taxa, 458 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	-1592.9377	3283.4638	0.4849	0.4849
GTRI	44	-1593.3223	3284.2330	0.3301	0.8151
GTRIG	45	-1592.7161	3285.4808	0.1769	0.9920
HKYG	40	-1602.6957	3293.2572	0.0036	0.9956
HKYI	40	-1603.1923	3294.2503	0.0022	0.9978
HKYIG	41	-1602.5871	3295.4530	0.0012	0.9990
SYMG	41	-1603.5345	3297.3478	0.0005	0.9995
SYMI	41	-1604.2486	3298.7761	0.0002	0.9997
SYMIG	42	-1603.4692	3299.6421	0.0001	0.9998
K2PG	37	-1610.0037	3300.7027	0.0001	0.9999
K2PI	37	-1610.7306	3302.1564	0.0000	1.0000
K2PIG	38	-1609.9370	3302.9481	0.0000	1.0000
F81G	39	-1627.6496	3340.7633	0.0000	1.0000
F81I	39	-1627.7731	3341.0103	0.0000	1.0000
F81IG	40	-1627.5375	3342.9406	0.0000	1.0000
JC69G	36	-1632.9808	3344.2895	0.0000	1.0000
JC69I	36	-1633.2341	3344.7959	0.0000	1.0000
JC69IG	37	-1632.9876	3346.6705	0.0000	1.0000
GTR	43	-1625.7999	3346.7399	0.0000	1.0000
HKY	39	-1633.9388	3353.3418	0.0000	1.0000
SYM	40	-1633.8460	3355.5578	0.0000	1.0000
K2P	36	-1640.2807	3358.8892	0.0000	1.0000
F81	38	-1656.7000	3396.4740	0.0000	1.0000
JC69	35	-1661.5972	3399.1660	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1592.9377	3273.8754	0.4657	0.4657
GTRI	44	-1593.3223	3274.6446	0.3170	0.7827
GTRIG	45	-1592.7161	3275.4322	0.2138	0.9966
HKYG	40	-1602.6957	3285.3915	0.0015	0.9980
HKYI	40	-1603.1923	3286.3846	0.0009	0.9989
HKYIG	41	-1602.5871	3287.1742	0.0006	0.9995
SYMG	41	-1603.5345	3289.0690	0.0002	0.9998
SYMI	41	-1604.2486	3290.4972	0.0001	0.9999
SYMIG	42	-1603.4692	3290.9384	0.0001	1.0000
K2PG	37	-1610.0037	3294.0075	0.0000	1.0000
K2PI	37	-1610.7306	3295.4612	0.0000	1.0000
K2PIG	38	-1609.9370	3295.8741	0.0000	1.0000
F81G	39	-1627.6496	3333.2992	0.0000	1.0000
F81I	39	-1627.7731	3333.5462	0.0000	1.0000
F81IG	40	-1627.5375	3335.0749	0.0000	1.0000
GTR	43	-1625.7999	3337.5998	0.0000	1.0000
JC69G	36	-1632.9808	3337.9617	0.0000	1.0000
JC69I	36	-1633.2341	3338.4681	0.0000	1.0000
JC69IG	37	-1632.9876	3339.9753	0.0000	1.0000
HKY	39	-1633.9388	3345.8776	0.0000	1.0000
SYM	40	-1633.8460	3347.6921	0.0000	1.0000
K2P	36	-1640.2807	3352.5614	0.0000	1.0000
F81	38	-1656.7000	3389.4000	0.0000	1.0000
JC69	35	-1661.5972	3393.1945	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1610.0037	3446.7016	0.5516	0.5516
K2PI	37	-1610.7306	3448.1553	0.2667	0.8183
HKYG	40	-1602.6957	3450.4662	0.0840	0.9023
HKYI	40	-1603.1923	3451.4593	0.0511	0.9534
K2PIG	38	-1609.9370	3452.6951	0.0276	0.9810
GTRG	44	-1592.9377	3455.4576	0.0069	0.9879
GTRI	44	-1593.3223	3456.2268	0.0047	0.9926
HKYIG	41	-1602.5871	3456.3758	0.0044	0.9970
SYMG	41	-1603.5345	3458.2706	0.0017	0.9987
SYMI	41	-1604.2486	3459.6989	0.0008	0.9995
GTRIG	45	-1592.7161	3461.1413	0.0004	0.9999
SYMIG	42	-1603.4692	3464.2669	0.0001	1.0000
JC69G	36	-1632.9808	3486.5290	0.0000	1.0000
JC69I	36	-1633.2341	3487.0354	0.0000	1.0000
JC69IG	37	-1632.9876	3492.6694	0.0000	1.0000
F81G	39	-1627.6496	3494.2471	0.0000	1.0000
F81I	39	-1627.7731	3494.4941	0.0000	1.0000
F81IG	40	-1627.5375	3500.1497	0.0000	1.0000
K2P	36	-1640.2807	3501.1287	0.0000	1.0000
HKY	39	-1633.9388	3506.8255	0.0000	1.0000
SYM	40	-1633.8460	3512.7668	0.0000	1.0000
GTR	43	-1625.7999	3515.0552	0.0000	1.0000
JC69	35	-1661.5972	3537.6349	0.0000	1.0000
F81	38	-1656.7000	3546.2211	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/chr9_5218.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5218.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/chr9_5218.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5218.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/chr9_5218.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_5218.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

