
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:44 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/chr7_10540.phylip" (19 taxa, 541 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-1784.0449	3664.0738	0.5435	0.5435
GTRI	44	-1784.6725	3665.3288	0.2902	0.8337
GTRIG	45	-1784.0397	3666.4430	0.1662	0.9999
SYMG	41	-1797.3672	3683.6361	0.0000	1.0000
SYMI	41	-1797.8885	3684.6787	0.0000	1.0000
SYMIG	42	-1797.3312	3685.9154	0.0000	1.0000
HKYG	40	-1801.0745	3688.7090	0.0000	1.0000
HKYI	40	-1801.4215	3689.4031	0.0000	1.0000
HKYIG	41	-1801.1071	3691.1161	0.0000	1.0000
GTR	43	-1801.1255	3695.8647	0.0000	1.0000
SYM	40	-1814.1906	3714.9412	0.0000	1.0000
HKY	39	-1821.8553	3727.9382	0.0000	1.0000
K2PI	37	-1830.8029	3741.1962	0.0000	1.0000
K2PG	37	-1830.9132	3741.4168	0.0000	1.0000
K2PIG	38	-1830.9682	3743.8408	0.0000	1.0000
K2P	36	-1855.3781	3788.0419	0.0000	1.0000
F81G	39	-1866.3139	3816.8553	0.0000	1.0000
F81I	39	-1866.7314	3817.6903	0.0000	1.0000
F81IG	40	-1866.3661	3819.2922	0.0000	1.0000
F81	38	-1895.2277	3872.3597	0.0000	1.0000
JC69I	36	-1911.8676	3901.0208	0.0000	1.0000
JC69G	36	-1912.0540	3901.3938	0.0000	1.0000
JC69IG	37	-1911.7966	3903.1836	0.0000	1.0000
JC69	35	-1933.9694	3942.9288	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1784.0449	3656.0899	0.5253	0.5253
GTRI	44	-1784.6725	3657.3449	0.2804	0.8057
GTRIG	45	-1784.0397	3658.0793	0.1943	1.0000
SYMG	41	-1797.3672	3676.7343	0.0000	1.0000
SYMI	41	-1797.8885	3677.7769	0.0000	1.0000
SYMIG	42	-1797.3312	3678.6624	0.0000	1.0000
HKYG	40	-1801.0745	3682.1490	0.0000	1.0000
HKYI	40	-1801.4215	3682.8431	0.0000	1.0000
HKYIG	41	-1801.1071	3684.2143	0.0000	1.0000
GTR	43	-1801.1255	3688.2510	0.0000	1.0000
SYM	40	-1814.1906	3708.3812	0.0000	1.0000
HKY	39	-1821.8553	3721.7107	0.0000	1.0000
K2PI	37	-1830.8029	3735.6057	0.0000	1.0000
K2PG	37	-1830.9132	3735.8264	0.0000	1.0000
K2PIG	38	-1830.9682	3737.9364	0.0000	1.0000
K2P	36	-1855.3781	3782.7562	0.0000	1.0000
F81G	39	-1866.3139	3810.6278	0.0000	1.0000
F81I	39	-1866.7314	3811.4628	0.0000	1.0000
F81IG	40	-1866.3661	3812.7322	0.0000	1.0000
F81	38	-1895.2277	3866.4553	0.0000	1.0000
JC69I	36	-1911.8676	3895.7351	0.0000	1.0000
JC69G	36	-1912.0540	3896.1081	0.0000	1.0000
JC69IG	37	-1911.7966	3897.5932	0.0000	1.0000
JC69	35	-1933.9694	3937.9387	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1784.0449	3845.0003	0.6129	0.6129
GTRI	44	-1784.6725	3846.2553	0.3273	0.9402
GTRIG	45	-1784.0397	3851.2832	0.0265	0.9667
SYMG	41	-1797.3672	3852.7645	0.0126	0.9793
SYMI	41	-1797.8885	3853.8071	0.0075	0.9868
HKYG	40	-1801.0745	3853.8858	0.0072	0.9940
HKYI	40	-1801.4215	3854.5799	0.0051	0.9991
SYMIG	42	-1797.3312	3858.9860	0.0006	0.9997
HKYIG	41	-1801.1071	3860.2445	0.0003	1.0000
GTR	43	-1801.1255	3872.8681	0.0000	1.0000
SYM	40	-1814.1906	3880.1180	0.0000	1.0000
HKY	39	-1821.8553	3889.1540	0.0000	1.0000
K2PI	37	-1830.8029	3894.4622	0.0000	1.0000
K2PG	37	-1830.9132	3894.6829	0.0000	1.0000
K2PIG	38	-1830.9682	3901.0863	0.0000	1.0000
K2P	36	-1855.3781	3937.3193	0.0000	1.0000
F81G	39	-1866.3139	3978.0711	0.0000	1.0000
F81I	39	-1866.7314	3978.9061	0.0000	1.0000
F81IG	40	-1866.3661	3984.4690	0.0000	1.0000
F81	38	-1895.2277	4029.6052	0.0000	1.0000
JC69I	36	-1911.8676	4050.2982	0.0000	1.0000
JC69G	36	-1912.0540	4050.6712	0.0000	1.0000
JC69IG	37	-1911.7966	4056.4497	0.0000	1.0000
JC69	35	-1933.9694	4088.2084	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/chr7_10540.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10540.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/chr7_10540.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10540.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10540.phylip = 1 - 541;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10540.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;


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End of Output

