
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:23 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/chr12_4543.phylip" (19 taxa, 405 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	-1730.1682	3559.3364	0.6286	0.6286
GTRIG	45	-1729.9993	3561.5307	0.2098	0.8385
GTRI	44	-1731.7493	3562.4987	0.1293	0.9678
HKYG	40	-1738.7518	3566.5145	0.0174	0.9852
HKYIG	41	-1738.3612	3568.2100	0.0074	0.9926
HKYI	40	-1739.6041	3568.2192	0.0074	1.0000
K2PG	37	-1754.8626	3591.3874	0.0000	1.0000
K2PI	37	-1755.3581	3592.3784	0.0000	1.0000
K2PIG	38	-1754.3202	3592.7387	0.0000	1.0000
SYMG	41	-1752.2045	3595.8967	0.0000	1.0000
SYMI	41	-1752.6297	3596.7469	0.0000	1.0000
SYMIG	42	-1751.7740	3597.5260	0.0000	1.0000
GTR	43	-1777.1325	3650.7470	0.0000	1.0000
HKY	39	-1786.0792	3658.7063	0.0000	1.0000
F81G	39	-1788.3312	3663.2104	0.0000	1.0000
F81I	39	-1788.4095	3663.3669	0.0000	1.0000
F81IG	40	-1787.6380	3664.2869	0.0000	1.0000
JC69I	36	-1800.8027	3680.8446	0.0000	1.0000
JC69G	36	-1800.9741	3681.1874	0.0000	1.0000
JC69IG	37	-1800.2214	3682.1049	0.0000	1.0000
K2P	36	-1805.7764	3690.7920	0.0000	1.0000
SYM	40	-1802.0938	3693.1985	0.0000	1.0000
F81	38	-1834.5934	3753.2851	0.0000	1.0000
JC69	35	-1848.9078	3774.6448	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1730.1682	3548.3364	0.6019	0.6019
GTRIG	45	-1729.9993	3549.9986	0.2622	0.8640
GTRI	44	-1731.7493	3551.4987	0.1238	0.9879
HKYG	40	-1738.7518	3557.5035	0.0062	0.9940
HKYIG	41	-1738.3612	3558.7224	0.0033	0.9974
HKYI	40	-1739.6041	3559.2082	0.0026	1.0000
K2PG	37	-1754.8626	3583.7253	0.0000	1.0000
K2PIG	38	-1754.3202	3584.6403	0.0000	1.0000
K2PI	37	-1755.3581	3584.7163	0.0000	1.0000
SYMG	41	-1752.2045	3586.4091	0.0000	1.0000
SYMI	41	-1752.6297	3587.2593	0.0000	1.0000
SYMIG	42	-1751.7740	3587.5481	0.0000	1.0000
GTR	43	-1777.1325	3640.2650	0.0000	1.0000
HKY	39	-1786.0792	3650.1584	0.0000	1.0000
F81G	39	-1788.3312	3654.6625	0.0000	1.0000
F81I	39	-1788.4095	3654.8189	0.0000	1.0000
F81IG	40	-1787.6380	3655.2760	0.0000	1.0000
JC69I	36	-1800.8027	3673.6055	0.0000	1.0000
JC69G	36	-1800.9741	3673.9483	0.0000	1.0000
JC69IG	37	-1800.2214	3674.4428	0.0000	1.0000
K2P	36	-1805.7764	3683.5529	0.0000	1.0000
SYM	40	-1802.0938	3684.1875	0.0000	1.0000
F81	38	-1834.5934	3745.1867	0.0000	1.0000
JC69	35	-1848.9078	3767.8156	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1738.7518	3717.6590	0.6483	0.6483
HKYI	40	-1739.6041	3719.3637	0.2765	0.9248
HKYIG	41	-1738.3612	3722.8818	0.0476	0.9724
GTRG	44	-1730.1682	3724.5075	0.0211	0.9935
GTRI	44	-1731.7493	3727.6697	0.0043	0.9979
GTRIG	45	-1729.9993	3730.1736	0.0012	0.9991
K2PG	37	-1754.8626	3731.8691	0.0005	0.9996
K2PI	37	-1755.3581	3732.8601	0.0003	1.0000
K2PIG	38	-1754.3202	3736.7880	0.0000	1.0000
SYMG	41	-1752.2045	3750.5684	0.0000	1.0000
SYMI	41	-1752.6297	3751.4187	0.0000	1.0000
SYMIG	42	-1751.7740	3755.7114	0.0000	1.0000
HKY	39	-1786.0792	3806.3100	0.0000	1.0000
F81G	39	-1788.3312	3810.8141	0.0000	1.0000
F81I	39	-1788.4095	3810.9705	0.0000	1.0000
GTR	43	-1777.1325	3812.4322	0.0000	1.0000
F81IG	40	-1787.6380	3815.4314	0.0000	1.0000
JC69I	36	-1800.8027	3817.7454	0.0000	1.0000
JC69G	36	-1800.9741	3818.0882	0.0000	1.0000
JC69IG	37	-1800.2214	3822.5866	0.0000	1.0000
K2P	36	-1805.7764	3827.6928	0.0000	1.0000
SYM	40	-1802.0938	3844.3430	0.0000	1.0000
F81	38	-1834.5934	3897.3344	0.0000	1.0000
JC69	35	-1848.9078	3907.9516	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/chr12_4543.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_4543.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/chr12_4543.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_4543.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/chr12_4543.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_4543.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

