
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:12 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_22045.phylip" (19 taxa, 463 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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	-1639.2188	3378.3656	0.3626	0.3626
GTRG	44	-1641.0554	3379.5845	0.1971	0.5597
GTRI	44	-1641.3815	3380.2367	0.1423	0.7020
HKYIG	41	-1645.0582	3380.2969	0.1380	0.8400
HKYI	40	-1646.7338	3381.2401	0.0861	0.9262
HKYG	40	-1646.8879	3381.5483	0.0738	1.0000
K2PIG	38	-1669.3674	3421.7254	0.0000	1.0000
K2PI	37	-1670.6957	3422.0079	0.0000	1.0000
K2PG	37	-1671.2742	3423.1648	0.0000	1.0000
SYMIG	42	-1666.2950	3425.1900	0.0000	1.0000
SYMI	41	-1667.6556	3425.4918	0.0000	1.0000
SYMG	41	-1667.8647	3425.9098	0.0000	1.0000
F81G	39	-1674.7019	3434.7796	0.0000	1.0000
F81IG	40	-1674.5239	3436.8204	0.0000	1.0000
F81I	39	-1675.9624	3437.3007	0.0000	1.0000
GTR	43	-1683.0437	3461.1183	0.0000	1.0000
HKY	39	-1690.2786	3465.9331	0.0000	1.0000
JC69G	36	-1694.6685	3467.5906	0.0000	1.0000
JC69IG	37	-1694.5849	3469.7863	0.0000	1.0000
JC69I	36	-1695.8809	3470.0153	0.0000	1.0000
K2P	36	-1716.5557	3511.3649	0.0000	1.0000
SYM	40	-1712.1435	3512.0595	0.0000	1.0000
F81	38	-1717.6231	3518.2367	0.0000	1.0000
JC69	35	-1739.3232	3554.5481	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1639.2188	3368.4375	0.4867	0.4867
GTRG	44	-1641.0554	3370.1108	0.2108	0.6975
GTRI	44	-1641.3815	3370.7631	0.1521	0.8496
HKYIG	41	-1645.0582	3372.1164	0.0773	0.9269
HKYI	40	-1646.7338	3373.4676	0.0394	0.9663
HKYG	40	-1646.8879	3373.7758	0.0337	1.0000
K2PIG	38	-1669.3674	3414.7348	0.0000	1.0000
K2PI	37	-1670.6957	3415.3914	0.0000	1.0000
K2PG	37	-1671.2742	3416.5483	0.0000	1.0000
SYMIG	42	-1666.2950	3416.5900	0.0000	1.0000
SYMI	41	-1667.6556	3417.3113	0.0000	1.0000
SYMG	41	-1667.8647	3417.7293	0.0000	1.0000
F81G	39	-1674.7019	3427.4038	0.0000	1.0000
F81IG	40	-1674.5239	3429.0479	0.0000	1.0000
F81I	39	-1675.9624	3429.9248	0.0000	1.0000
GTR	43	-1683.0437	3452.0873	0.0000	1.0000
HKY	39	-1690.2786	3458.5572	0.0000	1.0000
JC69G	36	-1694.6685	3461.3370	0.0000	1.0000
JC69IG	37	-1694.5849	3463.1698	0.0000	1.0000
JC69I	36	-1695.8809	3463.7618	0.0000	1.0000
SYM	40	-1712.1435	3504.2869	0.0000	1.0000
K2P	36	-1716.5557	3505.1114	0.0000	1.0000
F81	38	-1717.6231	3511.2462	0.0000	1.0000
JC69	35	-1739.3232	3548.6464	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1646.7338	3538.9767	0.4743	0.4743
HKYG	40	-1646.8879	3539.2849	0.4066	0.8809
HKYIG	41	-1645.0582	3541.7632	0.1178	0.9987
GTRG	44	-1641.0554	3552.1708	0.0006	0.9993
GTRI	44	-1641.3815	3552.8231	0.0005	0.9998
GTRIG	45	-1639.2188	3554.6352	0.0002	1.0000
K2PI	37	-1670.6957	3568.4873	0.0000	1.0000
K2PG	37	-1671.2742	3569.6442	0.0000	1.0000
K2PIG	38	-1669.3674	3571.9685	0.0000	1.0000
SYMI	41	-1667.6556	3586.9581	0.0000	1.0000
SYMG	41	-1667.8647	3587.3761	0.0000	1.0000
F81G	39	-1674.7019	3588.7751	0.0000	1.0000
SYMIG	42	-1666.2950	3590.3746	0.0000	1.0000
F81I	39	-1675.9624	3591.2962	0.0000	1.0000
F81IG	40	-1674.5239	3594.5570	0.0000	1.0000
JC69G	36	-1694.6685	3610.2952	0.0000	1.0000
JC69I	36	-1695.8809	3612.7199	0.0000	1.0000
JC69IG	37	-1694.5849	3616.2657	0.0000	1.0000
HKY	39	-1690.2786	3619.9285	0.0000	1.0000
GTR	43	-1683.0437	3630.0096	0.0000	1.0000
K2P	36	-1716.5557	3654.0696	0.0000	1.0000
F81	38	-1717.6231	3668.4798	0.0000	1.0000
SYM	40	-1712.1435	3669.7960	0.0000	1.0000
JC69	35	-1739.3232	3693.4669	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/chr2_22045.phylip = 1 - 463;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22045.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/chr2_22045.phylip = 1 - 463;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22045.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22045.phylip = 1 - 463;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22045.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

