
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:00 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_13491.phylip" (19 taxa, 922 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
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
SYMG	41	-3604.2608	7294.4352	0.4574	0.4574
SYMIG	42	-3603.8200	7295.7493	0.2371	0.6945
GTRG	44	-3601.7854	7296.0861	0.2003	0.8948
GTRIG	45	-3601.3348	7297.3956	0.1041	0.9989
K2PG	37	-3615.2738	7307.7286	0.0006	0.9995
K2PIG	38	-3614.7972	7308.9511	0.0003	0.9998
HKYG	40	-3613.9750	7311.6730	0.0001	0.9999
HKYIG	41	-3613.4870	7312.8876	0.0000	1.0000
SYMI	41	-3613.8909	7313.6954	0.0000	1.0000
GTRI	44	-3611.8338	7316.1830	0.0000	1.0000
K2PI	37	-3624.6686	7326.5183	0.0000	1.0000
HKYI	40	-3623.6333	7330.9897	0.0000	1.0000
JC69G	36	-3666.9378	7408.8859	0.0000	1.0000
JC69IG	37	-3666.7031	7410.5873	0.0000	1.0000
F81G	39	-3665.4215	7412.3804	0.0000	1.0000
F81IG	40	-3665.1752	7414.0735	0.0000	1.0000
JC69I	36	-3674.8462	7424.7025	0.0000	1.0000
F81I	39	-3673.5247	7428.5868	0.0000	1.0000
SYM	40	-3721.6955	7527.1140	0.0000	1.0000
GTR	43	-3719.5567	7529.4232	0.0000	1.0000
K2P	36	-3734.9755	7544.9611	0.0000	1.0000
HKY	39	-3734.0518	7549.6410	0.0000	1.0000
JC69	35	-3782.5651	7637.9744	0.0000	1.0000
F81	38	-3781.2866	7641.9300	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-3604.2608	7290.5215	0.3989	0.3989
GTRG	44	-3601.7854	7291.5707	0.2361	0.6350
SYMIG	42	-3603.8200	7291.6401	0.2280	0.8630
GTRIG	45	-3601.3348	7292.6695	0.1363	0.9993
K2PG	37	-3615.2738	7304.5476	0.0004	0.9996
K2PIG	38	-3614.7972	7305.5944	0.0002	0.9999
HKYG	40	-3613.9750	7307.9500	0.0001	0.9999
HKYIG	41	-3613.4870	7308.9740	0.0000	1.0000
SYMI	41	-3613.8909	7309.7818	0.0000	1.0000
GTRI	44	-3611.8338	7311.6676	0.0000	1.0000
K2PI	37	-3624.6686	7323.3373	0.0000	1.0000
HKYI	40	-3623.6333	7327.2666	0.0000	1.0000
JC69G	36	-3666.9378	7405.8757	0.0000	1.0000
JC69IG	37	-3666.7031	7407.4063	0.0000	1.0000
F81G	39	-3665.4215	7408.8429	0.0000	1.0000
F81IG	40	-3665.1752	7410.3504	0.0000	1.0000
JC69I	36	-3674.8462	7421.6924	0.0000	1.0000
F81I	39	-3673.5247	7425.0494	0.0000	1.0000
SYM	40	-3721.6955	7523.3910	0.0000	1.0000
GTR	43	-3719.5567	7525.1134	0.0000	1.0000
K2P	36	-3734.9755	7541.9509	0.0000	1.0000
HKY	39	-3734.0518	7546.1036	0.0000	1.0000
JC69	35	-3782.5651	7635.1302	0.0000	1.0000
F81	38	-3781.2866	7638.5732	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3615.2738	7483.1298	0.8863	0.8863
SYMG	41	-3604.2608	7488.4099	0.0632	0.9495
K2PIG	38	-3614.7972	7489.0031	0.0470	0.9965
SYMIG	42	-3603.8200	7494.3550	0.0032	0.9998
HKYG	40	-3613.9750	7501.0118	0.0001	0.9999
K2PI	37	-3624.6686	7501.9194	0.0001	1.0000
GTRG	44	-3601.7854	7503.9387	0.0000	1.0000
HKYIG	41	-3613.4870	7506.8624	0.0000	1.0000
SYMI	41	-3613.8909	7507.6701	0.0000	1.0000
GTRIG	45	-3601.3348	7509.8641	0.0000	1.0000
HKYI	40	-3623.6333	7520.3284	0.0000	1.0000
GTRI	44	-3611.8338	7524.0356	0.0000	1.0000
JC69G	36	-3666.9378	7579.6313	0.0000	1.0000
JC69IG	37	-3666.7031	7585.9884	0.0000	1.0000
JC69I	36	-3674.8462	7595.4480	0.0000	1.0000
F81G	39	-3665.4215	7597.0782	0.0000	1.0000
F81IG	40	-3665.1752	7603.4122	0.0000	1.0000
F81I	39	-3673.5247	7613.2846	0.0000	1.0000
K2P	36	-3734.9755	7715.7065	0.0000	1.0000
SYM	40	-3721.6955	7716.4528	0.0000	1.0000
GTR	43	-3719.5567	7732.6548	0.0000	1.0000
HKY	39	-3734.0518	7734.3389	0.0000	1.0000
JC69	35	-3782.5651	7804.0593	0.0000	1.0000
F81	38	-3781.2866	7821.9819	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13491.phylip = 1 - 922;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13491.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=Fixed(Equal);
END;


[Mrbayes block for the best AICc model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13491.phylip = 1 - 922;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13491.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=Fixed(Equal);
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/chr2_13491.phylip = 1 - 922;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_13491.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

