
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:08 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_5526.phylip" (19 taxa, 514 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	-1701.7251	3499.8938	0.6224	0.6224
GTRIG	45	-1701.1484	3501.1430	0.3333	0.9556
HKYIG	41	-1708.3191	3505.9348	0.0304	0.9860
GTRI	44	-1706.2234	3508.8903	0.0069	0.9929
HKYG	40	-1711.0397	3509.0138	0.0065	0.9994
HKYI	40	-1713.4959	3513.9262	0.0006	1.0000
K2PIG	38	-1724.6143	3531.4686	0.0000	1.0000
K2PG	37	-1726.2657	3532.4389	0.0000	1.0000
SYMIG	42	-1721.2173	3534.1034	0.0000	1.0000
SYMG	41	-1722.9100	3535.1167	0.0000	1.0000
K2PI	37	-1729.3895	3538.6865	0.0000	1.0000
SYMI	41	-1727.4859	3544.2684	0.0000	1.0000
F81G	39	-1746.5232	3577.6286	0.0000	1.0000
F81IG	40	-1745.4468	3577.8280	0.0000	1.0000
F81I	39	-1748.9960	3582.5742	0.0000	1.0000
GTR	43	-1748.9206	3591.8922	0.0000	1.0000
JC69IG	37	-1758.2238	3596.3551	0.0000	1.0000
JC69G	36	-1759.4306	3596.4460	0.0000	1.0000
HKY	39	-1756.2580	3597.0983	0.0000	1.0000
JC69I	36	-1760.1107	3597.8063	0.0000	1.0000
K2P	36	-1771.9754	3621.5357	0.0000	1.0000
SYM	40	-1768.6684	3624.2712	0.0000	1.0000
F81	38	-1789.2632	3660.7663	0.0000	1.0000
JC69	35	-1802.4970	3680.2660	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1701.7251	3491.4503	0.5886	0.5886
GTRIG	45	-1701.1484	3492.2969	0.3855	0.9741
HKYIG	41	-1708.3191	3498.6381	0.0162	0.9903
GTRI	44	-1706.2234	3500.4468	0.0066	0.9969
HKYG	40	-1711.0397	3502.0794	0.0029	0.9998
HKYI	40	-1713.4959	3506.9917	0.0002	1.0000
K2PIG	38	-1724.6143	3525.2286	0.0000	1.0000
SYMIG	42	-1721.2173	3526.4346	0.0000	1.0000
K2PG	37	-1726.2657	3526.5314	0.0000	1.0000
SYMG	41	-1722.9100	3527.8201	0.0000	1.0000
K2PI	37	-1729.3895	3532.7790	0.0000	1.0000
SYMI	41	-1727.4859	3536.9717	0.0000	1.0000
F81IG	40	-1745.4468	3570.8935	0.0000	1.0000
F81G	39	-1746.5232	3571.0464	0.0000	1.0000
F81I	39	-1748.9960	3575.9919	0.0000	1.0000
GTR	43	-1748.9206	3583.8411	0.0000	1.0000
JC69IG	37	-1758.2238	3590.4475	0.0000	1.0000
HKY	39	-1756.2580	3590.5160	0.0000	1.0000
JC69G	36	-1759.4306	3590.8611	0.0000	1.0000
JC69I	36	-1760.1107	3592.2214	0.0000	1.0000
K2P	36	-1771.9754	3615.9508	0.0000	1.0000
SYM	40	-1768.6684	3617.3368	0.0000	1.0000
F81	38	-1789.2632	3654.5263	0.0000	1.0000
JC69	35	-1802.4970	3674.9940	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1711.0397	3671.7683	0.5540	0.5540
HKYIG	41	-1708.3191	3672.5693	0.3712	0.9251
HKYI	40	-1713.4959	3676.6807	0.0475	0.9726
GTRG	44	-1701.7251	3678.1081	0.0233	0.9959
GTRIG	45	-1701.1484	3683.1969	0.0018	0.9977
K2PG	37	-1726.2657	3683.4936	0.0016	0.9993
K2PIG	38	-1724.6143	3686.4331	0.0004	0.9997
GTRI	44	-1706.2234	3687.1047	0.0003	0.9999
K2PI	37	-1729.3895	3689.7412	0.0001	1.0000
SYMG	41	-1722.9100	3701.7512	0.0000	1.0000
SYMIG	42	-1721.2173	3704.6080	0.0000	1.0000
SYMI	41	-1727.4859	3710.9029	0.0000	1.0000
F81G	39	-1746.5232	3736.4931	0.0000	1.0000
F81IG	40	-1745.4468	3740.5824	0.0000	1.0000
F81I	39	-1748.9960	3741.4386	0.0000	1.0000
JC69G	36	-1759.4306	3743.5811	0.0000	1.0000
JC69I	36	-1760.1107	3744.9415	0.0000	1.0000
JC69IG	37	-1758.2238	3747.4098	0.0000	1.0000
HKY	39	-1756.2580	3755.9627	0.0000	1.0000
GTR	43	-1748.9206	3766.2567	0.0000	1.0000
K2P	36	-1771.9754	3768.6709	0.0000	1.0000
SYM	40	-1768.6684	3787.0257	0.0000	1.0000
F81	38	-1789.2632	3815.7308	0.0000	1.0000
JC69	35	-1802.4970	3823.4718	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/chr2_5526.phylip = 1 - 514;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5526.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/chr2_5526.phylip = 1 - 514;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5526.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/chr2_5526.phylip = 1 - 514;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5526.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

