
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:54 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/chr5_10327.phylip" (19 taxa, 1013 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	-4729.3524	9550.7956	0.4885	0.4885
HKYG	40	-4734.3399	9552.0543	0.2603	0.7488
GTRIG	45	-4729.3525	9552.9862	0.1634	0.9121
HKYIG	41	-4734.3399	9554.2266	0.0879	1.0000
HKYI	40	-4750.6751	9584.7246	0.0000	1.0000
GTRI	44	-4747.1303	9586.3515	0.0000	1.0000
K2PG	37	-4773.3236	9623.5313	0.0000	1.0000
SYMG	41	-4769.3808	9624.3085	0.0000	1.0000
K2PIG	38	-4773.3235	9625.6902	0.0000	1.0000
SYMIG	42	-4769.3808	9626.4853	0.0000	1.0000
K2PI	37	-4787.1680	9651.2200	0.0000	1.0000
SYMI	41	-4783.3840	9652.3148	0.0000	1.0000
HKY	39	-4805.6830	9692.5726	0.0000	1.0000
GTR	43	-4801.3473	9692.5997	0.0000	1.0000
K2P	36	-4846.8591	9768.4478	0.0000	1.0000
SYM	40	-4844.1136	9771.6016	0.0000	1.0000
F81G	39	-4897.0999	9875.4063	0.0000	1.0000
F81IG	40	-4896.5572	9876.4890	0.0000	1.0000
F81I	39	-4913.9369	9909.0804	0.0000	1.0000
JC69G	36	-4924.9693	9924.6680	0.0000	1.0000
JC69IG	37	-4924.9693	9926.8228	0.0000	1.0000
JC69I	36	-4936.2364	9947.2023	0.0000	1.0000
F81	38	-4964.8356	10008.7142	0.0000	1.0000
JC69	35	-4989.0381	10050.6556	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4729.3524	9546.7047	0.5327	0.5327
HKYG	40	-4734.3399	9548.6798	0.1984	0.7311
GTRIG	45	-4729.3525	9548.7050	0.1959	0.9270
HKYIG	41	-4734.3399	9550.6797	0.0730	1.0000
HKYI	40	-4750.6751	9581.3502	0.0000	1.0000
GTRI	44	-4747.1303	9582.2606	0.0000	1.0000
K2PG	37	-4773.3236	9620.6472	0.0000	1.0000
SYMG	41	-4769.3808	9620.7616	0.0000	1.0000
K2PIG	38	-4773.3235	9622.6471	0.0000	1.0000
SYMIG	42	-4769.3808	9622.7616	0.0000	1.0000
K2PI	37	-4787.1680	9648.3359	0.0000	1.0000
SYMI	41	-4783.3840	9648.7679	0.0000	1.0000
GTR	43	-4801.3473	9688.6947	0.0000	1.0000
HKY	39	-4805.6830	9689.3660	0.0000	1.0000
K2P	36	-4846.8591	9765.7183	0.0000	1.0000
SYM	40	-4844.1136	9768.2272	0.0000	1.0000
F81G	39	-4897.0999	9872.1997	0.0000	1.0000
F81IG	40	-4896.5572	9873.1145	0.0000	1.0000
F81I	39	-4913.9369	9905.8739	0.0000	1.0000
JC69G	36	-4924.9693	9921.9385	0.0000	1.0000
JC69IG	37	-4924.9693	9923.9387	0.0000	1.0000
JC69I	36	-4936.2364	9944.4728	0.0000	1.0000
F81	38	-4964.8356	10005.6711	0.0000	1.0000
JC69	35	-4989.0381	10048.0763	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4734.3399	9745.5066	0.9694	0.9694
HKYIG	41	-4734.3399	9752.4273	0.0305	0.9999
GTRG	44	-4729.3524	9763.2142	0.0001	1.0000
GTRIG	45	-4729.3525	9770.1352	0.0000	1.0000
HKYI	40	-4750.6751	9778.1770	0.0000	1.0000
GTRI	44	-4747.1303	9798.7701	0.0000	1.0000
K2PG	37	-4773.3236	9802.7120	0.0000	1.0000
K2PIG	38	-4773.3235	9809.6326	0.0000	1.0000
SYMG	41	-4769.3808	9822.5092	0.0000	1.0000
SYMIG	42	-4769.3808	9829.4298	0.0000	1.0000
K2PI	37	-4787.1680	9830.4007	0.0000	1.0000
SYMI	41	-4783.3840	9850.5154	0.0000	1.0000
HKY	39	-4805.6830	9881.2722	0.0000	1.0000
GTR	43	-4801.3473	9900.2836	0.0000	1.0000
K2P	36	-4846.8591	9942.8625	0.0000	1.0000
SYM	40	-4844.1136	9965.0540	0.0000	1.0000
F81G	39	-4897.0999	10064.1059	0.0000	1.0000
F81IG	40	-4896.5572	10069.9414	0.0000	1.0000
F81I	39	-4913.9369	10097.7800	0.0000	1.0000
JC69G	36	-4924.9693	10099.0827	0.0000	1.0000
JC69IG	37	-4924.9693	10106.0035	0.0000	1.0000
JC69I	36	-4936.2364	10121.6170	0.0000	1.0000
F81	38	-4964.8356	10192.6566	0.0000	1.0000
JC69	35	-4989.0381	10220.2998	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/chr5_10327.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10327.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/chr5_10327.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10327.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/chr5_10327.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10327.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

