
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:04 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_10997.phylip" (19 taxa, 742 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1736.0104	3567.9691	0.5350	0.5350
GTRG	44	-1737.7456	3569.1728	0.2931	0.8281
GTRI	44	-1738.2802	3570.2418	0.1717	0.9998
HKYIG	41	-1749.4654	3585.8509	0.0001	0.9999
HKYG	40	-1750.7445	3586.1681	0.0001	1.0000
HKYI	40	-1750.9582	3586.5953	0.0000	1.0000
GTR	43	-1764.8732	3621.1676	0.0000	1.0000
HKY	39	-1778.9071	3640.2586	0.0000	1.0000
F81G	39	-1781.2145	3644.8735	0.0000	1.0000
F81I	39	-1781.2693	3644.9830	0.0000	1.0000
F81IG	40	-1780.1952	3645.0694	0.0000	1.0000
F81	38	-1809.6845	3699.5851	0.0000	1.0000
SYMIG	42	-1805.5187	3700.2047	0.0000	1.0000
SYMG	41	-1808.1510	3703.2220	0.0000	1.0000
SYMI	41	-1808.2729	3703.4658	0.0000	1.0000
K2PIG	38	-1814.0385	3708.2932	0.0000	1.0000
K2PI	37	-1815.2784	3708.5511	0.0000	1.0000
K2PG	37	-1815.4346	3708.8635	0.0000	1.0000
JC69I	36	-1839.8712	3755.5211	0.0000	1.0000
JC69IG	37	-1838.7743	3755.5430	0.0000	1.0000
JC69G	36	-1839.9483	3755.6754	0.0000	1.0000
SYM	40	-1836.7532	3758.1853	0.0000	1.0000
K2P	36	-1846.1417	3768.0621	0.0000	1.0000
JC69	35	-1869.8387	3813.2468	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1736.0104	3562.0208	0.5680	0.5680
GTRG	44	-1737.7456	3563.4913	0.2723	0.8403
GTRI	44	-1738.2802	3564.5603	0.1596	0.9999
HKYIG	41	-1749.4654	3580.9309	0.0000	0.9999
HKYG	40	-1750.7445	3581.4891	0.0000	1.0000
HKYI	40	-1750.9582	3581.9163	0.0000	1.0000
GTR	43	-1764.8732	3615.7464	0.0000	1.0000
HKY	39	-1778.9071	3635.8142	0.0000	1.0000
F81IG	40	-1780.1952	3640.3903	0.0000	1.0000
F81G	39	-1781.2145	3640.4291	0.0000	1.0000
F81I	39	-1781.2693	3640.5385	0.0000	1.0000
SYMIG	42	-1805.5187	3695.0373	0.0000	1.0000
F81	38	-1809.6845	3695.3689	0.0000	1.0000
SYMG	41	-1808.1510	3698.3020	0.0000	1.0000
SYMI	41	-1808.2729	3698.5458	0.0000	1.0000
K2PIG	38	-1814.0385	3704.0770	0.0000	1.0000
K2PI	37	-1815.2784	3704.5567	0.0000	1.0000
K2PG	37	-1815.4346	3704.8692	0.0000	1.0000
JC69IG	37	-1838.7743	3751.5487	0.0000	1.0000
JC69I	36	-1839.8712	3751.7423	0.0000	1.0000
JC69G	36	-1839.9483	3751.8967	0.0000	1.0000
SYM	40	-1836.7532	3753.5063	0.0000	1.0000
K2P	36	-1846.1417	3764.2834	0.0000	1.0000
JC69	35	-1869.8387	3809.6774	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1750.7445	3765.8630	0.2959	0.2959
HKYI	40	-1750.9582	3766.2903	0.2390	0.5349
GTRG	44	-1737.7456	3766.3026	0.2375	0.7724
GTRI	44	-1738.2802	3767.3717	0.1392	0.9115
GTRIG	45	-1736.0104	3769.4415	0.0494	0.9610
HKYIG	41	-1749.4654	3769.9142	0.0390	1.0000
GTR	43	-1764.8732	3813.9484	0.0000	1.0000
HKY	39	-1778.9071	3815.5788	0.0000	1.0000
F81G	39	-1781.2145	3820.1937	0.0000	1.0000
F81I	39	-1781.2693	3820.3031	0.0000	1.0000
F81IG	40	-1780.1952	3824.7643	0.0000	1.0000
F81	38	-1809.6845	3870.5242	0.0000	1.0000
K2PI	37	-1815.2784	3875.1027	0.0000	1.0000
K2PG	37	-1815.4346	3875.4151	0.0000	1.0000
K2PIG	38	-1814.0385	3879.2322	0.0000	1.0000
SYMG	41	-1808.1510	3887.2853	0.0000	1.0000
SYMI	41	-1808.2729	3887.5291	0.0000	1.0000
SYMIG	42	-1805.5187	3888.6300	0.0000	1.0000
JC69I	36	-1839.8712	3917.6789	0.0000	1.0000
JC69G	36	-1839.9483	3917.8333	0.0000	1.0000
JC69IG	37	-1838.7743	3922.0946	0.0000	1.0000
K2P	36	-1846.1417	3930.2200	0.0000	1.0000
SYM	40	-1836.7532	3937.8803	0.0000	1.0000
JC69	35	-1869.8387	3971.0046	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10997.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10997.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10997.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10997.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr7_10997.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10997.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

