
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:12 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/chr1_1098.phylip" (19 taxa, 585 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1705.6501	3506.6336	0.3679	0.3679
GTRI	44	-1705.9445	3507.2223	0.2741	0.6420
HKYG	40	-1711.3673	3508.7641	0.1268	0.7688
GTRIG	45	-1705.6438	3508.9685	0.1145	0.8832
HKYI	40	-1711.9420	3509.9134	0.0714	0.9546
HKYIG	41	-1711.2382	3510.8190	0.0454	1.0000
K2PG	37	-1725.7910	3530.7227	0.0000	1.0000
K2PI	37	-1726.1914	3531.5235	0.0000	1.0000
K2PIG	38	-1725.7137	3532.8561	0.0000	1.0000
SYMG	41	-1724.0639	3536.4703	0.0000	1.0000
SYMI	41	-1724.4287	3537.1999	0.0000	1.0000
SYMIG	42	-1724.0037	3538.6717	0.0000	1.0000
HKY	39	-1742.0304	3567.7857	0.0000	1.0000
F81G	39	-1742.1000	3567.9248	0.0000	1.0000
GTR	43	-1737.6661	3568.3266	0.0000	1.0000
F81I	39	-1742.3677	3568.4602	0.0000	1.0000
F81IG	40	-1742.1148	3570.2591	0.0000	1.0000
JC69G	36	-1754.4621	3585.7855	0.0000	1.0000
JC69I	36	-1754.7162	3586.2938	0.0000	1.0000
JC69IG	37	-1754.4736	3588.0879	0.0000	1.0000
K2P	36	-1756.2921	3589.4456	0.0000	1.0000
SYM	40	-1754.7060	3595.4414	0.0000	1.0000
F81	38	-1771.5979	3624.6244	0.0000	1.0000
JC69	35	-1784.1390	3642.8682	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1705.6501	3499.3003	0.4047	0.4047
GTRI	44	-1705.9445	3499.8890	0.3015	0.7062
GTRIG	45	-1705.6438	3501.2876	0.1498	0.8560
HKYG	40	-1711.3673	3502.7347	0.0727	0.9287
HKYI	40	-1711.9420	3503.8840	0.0409	0.9696
HKYIG	41	-1711.2382	3504.4764	0.0304	1.0000
K2PG	37	-1725.7910	3525.5820	0.0000	1.0000
K2PI	37	-1726.1914	3526.3827	0.0000	1.0000
K2PIG	38	-1725.7137	3527.4275	0.0000	1.0000
SYMG	41	-1724.0639	3530.1277	0.0000	1.0000
SYMI	41	-1724.4287	3530.8574	0.0000	1.0000
SYMIG	42	-1724.0037	3532.0075	0.0000	1.0000
GTR	43	-1737.6661	3561.3321	0.0000	1.0000
HKY	39	-1742.0304	3562.0609	0.0000	1.0000
F81G	39	-1742.1000	3562.2000	0.0000	1.0000
F81I	39	-1742.3677	3562.7355	0.0000	1.0000
F81IG	40	-1742.1148	3564.2296	0.0000	1.0000
JC69G	36	-1754.4621	3580.9242	0.0000	1.0000
JC69I	36	-1754.7162	3581.4324	0.0000	1.0000
JC69IG	37	-1754.4736	3582.9472	0.0000	1.0000
K2P	36	-1756.2921	3584.5843	0.0000	1.0000
SYM	40	-1754.7060	3589.4120	0.0000	1.0000
F81	38	-1771.5979	3619.1958	0.0000	1.0000
JC69	35	-1784.1390	3638.2780	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1711.3673	3677.5992	0.6155	0.6155
HKYI	40	-1711.9420	3678.7485	0.3465	0.9619
HKYIG	41	-1711.2382	3683.7125	0.0290	0.9909
K2PG	37	-1725.7910	3687.3316	0.0047	0.9956
K2PI	37	-1726.1914	3688.1324	0.0032	0.9988
GTRG	44	-1705.6501	3691.6512	0.0005	0.9994
GTRI	44	-1705.9445	3692.2399	0.0004	0.9998
K2PIG	38	-1725.7137	3693.5488	0.0002	1.0000
GTRIG	45	-1705.6438	3698.0102	0.0000	1.0000
SYMG	41	-1724.0639	3709.3638	0.0000	1.0000
SYMI	41	-1724.4287	3710.0935	0.0000	1.0000
SYMIG	42	-1724.0037	3715.6152	0.0000	1.0000
HKY	39	-1742.0304	3732.5538	0.0000	1.0000
F81G	39	-1742.1000	3732.6929	0.0000	1.0000
F81I	39	-1742.3677	3733.2283	0.0000	1.0000
JC69G	36	-1754.4621	3738.3022	0.0000	1.0000
JC69I	36	-1754.7162	3738.8105	0.0000	1.0000
F81IG	40	-1742.1148	3739.0941	0.0000	1.0000
K2P	36	-1756.2921	3741.9623	0.0000	1.0000
JC69IG	37	-1754.4736	3744.6968	0.0000	1.0000
GTR	43	-1737.6661	3749.3114	0.0000	1.0000
SYM	40	-1754.7060	3764.2765	0.0000	1.0000
F81	38	-1771.5979	3785.3171	0.0000	1.0000
JC69	35	-1784.1390	3791.2844	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/chr1_1098.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1098.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/chr1_1098.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1098.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1098.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1098.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

