
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:29 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_30599.phylip" (19 taxa, 472 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	-1688.8145	3474.9031	0.5743	0.5743
HKYG	40	-1694.8320	3477.2743	0.1755	0.7498
GTRIG	45	-1688.8149	3477.3480	0.1691	0.9189
HKYIG	41	-1694.8352	3479.6798	0.0527	0.9716
GTRI	44	-1692.0854	3481.4448	0.0218	0.9935
HKYI	40	-1698.1209	3483.8520	0.0065	1.0000
GTR	43	-1706.8686	3508.5783	0.0000	1.0000
HKY	39	-1712.8617	3510.9456	0.0000	1.0000
F81G	39	-1721.6465	3528.5153	0.0000	1.0000
SYMG	41	-1719.2547	3528.5187	0.0000	1.0000
F81IG	40	-1721.6464	3530.9031	0.0000	1.0000
SYMIG	42	-1719.2599	3530.9395	0.0000	1.0000
K2PG	37	-1725.7979	3532.0750	0.0000	1.0000
SYMI	41	-1721.5229	3533.0551	0.0000	1.0000
F81I	39	-1724.1388	3533.4998	0.0000	1.0000
K2PIG	38	-1725.7988	3534.4428	0.0000	1.0000
K2PI	37	-1728.6908	3537.8608	0.0000	1.0000
SYM	40	-1737.4986	3562.6075	0.0000	1.0000
F81	38	-1740.0722	3562.9896	0.0000	1.0000
K2P	36	-1745.4108	3568.9458	0.0000	1.0000
JC69G	36	-1753.0894	3584.3029	0.0000	1.0000
JC69IG	37	-1753.0894	3586.6581	0.0000	1.0000
JC69I	36	-1755.3209	3588.7659	0.0000	1.0000
JC69	35	-1771.2419	3618.2635	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1688.8145	3465.6291	0.6280	0.6280
GTRIG	45	-1688.8149	3467.6297	0.2309	0.8589
HKYG	40	-1694.8320	3469.6641	0.0835	0.9424
HKYIG	41	-1694.8352	3471.6705	0.0306	0.9730
GTRI	44	-1692.0854	3472.1708	0.0238	0.9969
HKYI	40	-1698.1209	3476.2418	0.0031	1.0000
GTR	43	-1706.8686	3499.7372	0.0000	1.0000
HKY	39	-1712.8617	3503.7234	0.0000	1.0000
SYMG	41	-1719.2547	3520.5094	0.0000	1.0000
F81G	39	-1721.6465	3521.2931	0.0000	1.0000
SYMIG	42	-1719.2599	3522.5199	0.0000	1.0000
F81IG	40	-1721.6464	3523.2929	0.0000	1.0000
SYMI	41	-1721.5229	3525.0458	0.0000	1.0000
K2PG	37	-1725.7979	3525.5957	0.0000	1.0000
F81I	39	-1724.1388	3526.2775	0.0000	1.0000
K2PIG	38	-1725.7988	3527.5975	0.0000	1.0000
K2PI	37	-1728.6908	3531.3815	0.0000	1.0000
SYM	40	-1737.4986	3554.9973	0.0000	1.0000
F81	38	-1740.0722	3556.1444	0.0000	1.0000
K2P	36	-1745.4108	3562.8216	0.0000	1.0000
JC69G	36	-1753.0894	3578.1788	0.0000	1.0000
JC69IG	37	-1753.0894	3580.1789	0.0000	1.0000
JC69I	36	-1755.3209	3582.6417	0.0000	1.0000
JC69	35	-1771.2419	3612.4837	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1694.8320	3635.9432	0.9215	0.9215
HKYIG	41	-1694.8352	3642.1066	0.0423	0.9638
HKYI	40	-1698.1209	3642.5209	0.0344	0.9982
GTRG	44	-1688.8145	3648.5362	0.0017	0.9999
GTRIG	45	-1688.8149	3654.6938	0.0001	0.9999
GTRI	44	-1692.0854	3655.0779	0.0001	1.0000
HKY	39	-1712.8617	3665.8456	0.0000	1.0000
GTR	43	-1706.8686	3678.4873	0.0000	1.0000
K2PG	37	-1725.7979	3679.4039	0.0000	1.0000
F81G	39	-1721.6465	3683.4152	0.0000	1.0000
K2PI	37	-1728.6908	3685.1897	0.0000	1.0000
K2PIG	38	-1725.7988	3685.5627	0.0000	1.0000
F81I	39	-1724.1388	3688.3997	0.0000	1.0000
F81IG	40	-1721.6464	3689.5720	0.0000	1.0000
SYMG	41	-1719.2547	3690.9455	0.0000	1.0000
SYMI	41	-1721.5229	3695.4819	0.0000	1.0000
SYMIG	42	-1719.2599	3697.1130	0.0000	1.0000
K2P	36	-1745.4108	3712.4729	0.0000	1.0000
F81	38	-1740.0722	3714.1096	0.0000	1.0000
SYM	40	-1737.4986	3721.2765	0.0000	1.0000
JC69G	36	-1753.0894	3727.8300	0.0000	1.0000
JC69I	36	-1755.3209	3732.2930	0.0000	1.0000
JC69IG	37	-1753.0894	3733.9871	0.0000	1.0000
JC69	35	-1771.2419	3757.9780	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_30599.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30599.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_30599.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30599.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_30599.phylip = 1 - 472;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30599.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

