
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:55 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_9094.phylip" (19 taxa, 536 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	-1600.8259	3297.7170	0.5704	0.5704
GTRIG	45	-1600.1810	3298.8109	0.3301	0.9004
GTRI	44	-1602.6000	3301.2651	0.0968	0.9972
HKYG	40	-1611.4870	3309.6003	0.0015	0.9987
HKYIG	41	-1610.7487	3310.4692	0.0010	0.9996
HKYI	40	-1612.9357	3312.4977	0.0004	1.0000
SYMG	41	-1618.9709	3326.9135	0.0000	1.0000
SYMIG	42	-1618.2625	3327.8516	0.0000	1.0000
K2PG	37	-1624.9552	3329.5569	0.0000	1.0000
SYMI	41	-1620.4254	3329.8224	0.0000	1.0000
K2PIG	38	-1624.1660	3330.2957	0.0000	1.0000
K2PI	37	-1626.3856	3332.4178	0.0000	1.0000
GTR	43	-1638.3210	3370.3331	0.0000	1.0000
HKY	39	-1648.3456	3380.9814	0.0000	1.0000
SYM	40	-1654.8050	3396.2364	0.0000	1.0000
K2P	36	-1661.6789	3400.6966	0.0000	1.0000
F81G	39	-1664.7027	3413.6957	0.0000	1.0000
F81IG	40	-1664.0018	3414.6298	0.0000	1.0000
F81I	39	-1666.1893	3416.6690	0.0000	1.0000
JC69G	36	-1675.3391	3428.0169	0.0000	1.0000
JC69IG	37	-1674.6228	3428.8921	0.0000	1.0000
JC69I	36	-1676.8203	3430.9792	0.0000	1.0000
F81	38	-1699.6813	3481.3264	0.0000	1.0000
JC69	35	-1709.9614	3494.9629	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1600.8259	3289.6518	0.5338	0.5338
GTRIG	45	-1600.1810	3290.3620	0.3743	0.9081
GTRI	44	-1602.6000	3293.1999	0.0906	0.9986
HKYG	40	-1611.4870	3302.9740	0.0007	0.9993
HKYIG	41	-1610.7487	3303.4975	0.0005	0.9998
HKYI	40	-1612.9357	3305.8714	0.0002	1.0000
SYMG	41	-1618.9709	3319.9419	0.0000	1.0000
SYMIG	42	-1618.2625	3320.5250	0.0000	1.0000
SYMI	41	-1620.4254	3322.8508	0.0000	1.0000
K2PG	37	-1624.9552	3323.9103	0.0000	1.0000
K2PIG	38	-1624.1660	3324.3320	0.0000	1.0000
K2PI	37	-1626.3856	3326.7712	0.0000	1.0000
GTR	43	-1638.3210	3362.6421	0.0000	1.0000
HKY	39	-1648.3456	3374.6911	0.0000	1.0000
SYM	40	-1654.8050	3389.6101	0.0000	1.0000
K2P	36	-1661.6789	3395.3579	0.0000	1.0000
F81G	39	-1664.7027	3407.4054	0.0000	1.0000
F81IG	40	-1664.0018	3408.0035	0.0000	1.0000
F81I	39	-1666.1893	3410.3786	0.0000	1.0000
JC69G	36	-1675.3391	3422.6782	0.0000	1.0000
JC69IG	37	-1674.6228	3423.2455	0.0000	1.0000
JC69I	36	-1676.8203	3425.6405	0.0000	1.0000
F81	38	-1699.6813	3475.3626	0.0000	1.0000
JC69	35	-1709.9614	3489.9229	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1611.4870	3474.3394	0.6516	0.6516
HKYI	40	-1612.9357	3477.2368	0.1530	0.8047
GTRG	44	-1600.8259	3478.1537	0.0968	0.9014
HKYIG	41	-1610.7487	3479.1470	0.0589	0.9603
GTRI	44	-1602.6000	3481.7018	0.0164	0.9767
K2PG	37	-1624.9552	3482.4233	0.0114	0.9882
GTRIG	45	-1600.1810	3483.1480	0.0080	0.9962
K2PI	37	-1626.3856	3485.2842	0.0027	0.9989
K2PIG	38	-1624.1660	3487.1291	0.0011	1.0000
SYMG	41	-1618.9709	3495.5914	0.0000	1.0000
SYMI	41	-1620.4254	3498.5003	0.0000	1.0000
SYMIG	42	-1618.2625	3500.4587	0.0000	1.0000
HKY	39	-1648.3456	3541.7724	0.0000	1.0000
GTR	43	-1638.3210	3546.8598	0.0000	1.0000
K2P	36	-1661.6789	3549.5867	0.0000	1.0000
SYM	40	-1654.8050	3560.9755	0.0000	1.0000
F81G	39	-1664.7027	3574.4866	0.0000	1.0000
JC69G	36	-1675.3391	3576.9070	0.0000	1.0000
F81I	39	-1666.1893	3577.4599	0.0000	1.0000
F81IG	40	-1664.0018	3579.3689	0.0000	1.0000
JC69I	36	-1676.8203	3579.8693	0.0000	1.0000
JC69IG	37	-1674.6228	3581.7585	0.0000	1.0000
F81	38	-1699.6813	3638.1597	0.0000	1.0000
JC69	35	-1709.9614	3639.8676	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/chr7_9094.phylip = 1 - 536;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9094.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/chr7_9094.phylip = 1 - 536;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9094.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/chr7_9094.phylip = 1 - 536;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9094.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

