
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:04 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_4601.phylip" (19 taxa, 493 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1608.0404	3312.9202	0.2610	0.2610
GTRG	44	-1608.0693	3312.9779	0.2536	0.5146
HKYG	40	-1613.1022	3313.4610	0.1992	0.7137
HKYI	40	-1613.5261	3314.3089	0.1303	0.8440
GTRIG	45	-1607.9081	3315.0779	0.0887	0.9328
HKYIG	41	-1613.0067	3315.6497	0.0667	0.9994
K2PG	37	-1623.5737	3327.3275	0.0002	0.9996
K2PI	37	-1623.7478	3327.6758	0.0002	0.9998
K2PIG	38	-1623.4725	3329.4737	0.0001	0.9999
SYMI	41	-1620.0490	3329.7343	0.0001	0.9999
SYMG	41	-1620.1263	3329.8889	0.0001	1.0000
SYMIG	42	-1619.9450	3331.9167	0.0000	1.0000
GTR	43	-1623.0528	3340.5332	0.0000	1.0000
HKY	39	-1627.9582	3340.8038	0.0000	1.0000
K2P	36	-1638.7316	3355.3054	0.0000	1.0000
SYM	40	-1634.9043	3357.0652	0.0000	1.0000
F81G	39	-1646.4341	3377.7556	0.0000	1.0000
F81I	39	-1646.4806	3377.8485	0.0000	1.0000
F81IG	40	-1646.3253	3379.9073	0.0000	1.0000
JC69G	36	-1655.0596	3387.9613	0.0000	1.0000
JC69I	36	-1655.1035	3388.0491	0.0000	1.0000
JC69IG	37	-1654.9512	3390.0826	0.0000	1.0000
F81	38	-1660.8583	3404.2453	0.0000	1.0000
JC69	35	-1669.6709	3414.8560	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1608.0404	3304.0809	0.3221	0.3221
GTRG	44	-1608.0693	3304.1386	0.3130	0.6351
GTRIG	45	-1607.9081	3305.8162	0.1353	0.7704
HKYG	40	-1613.1022	3306.2043	0.1114	0.8818
HKYI	40	-1613.5261	3307.0523	0.0729	0.9547
HKYIG	41	-1613.0067	3308.0134	0.0451	0.9998
K2PG	37	-1623.5737	3321.1473	0.0001	0.9998
K2PI	37	-1623.7478	3321.4956	0.0001	0.9999
SYMI	41	-1620.0490	3322.0980	0.0000	0.9999
SYMG	41	-1620.1263	3322.2526	0.0000	1.0000
K2PIG	38	-1623.4725	3322.9451	0.0000	1.0000
SYMIG	42	-1619.9450	3323.8901	0.0000	1.0000
GTR	43	-1623.0528	3332.1056	0.0000	1.0000
HKY	39	-1627.9582	3333.9164	0.0000	1.0000
K2P	36	-1638.7316	3349.4633	0.0000	1.0000
SYM	40	-1634.9043	3349.8086	0.0000	1.0000
F81G	39	-1646.4341	3370.8681	0.0000	1.0000
F81I	39	-1646.4806	3370.9611	0.0000	1.0000
F81IG	40	-1646.3253	3372.6507	0.0000	1.0000
JC69G	36	-1655.0596	3382.1192	0.0000	1.0000
JC69I	36	-1655.1035	3382.2070	0.0000	1.0000
JC69IG	37	-1654.9512	3383.9023	0.0000	1.0000
F81	38	-1660.8583	3397.7167	0.0000	1.0000
JC69	35	-1669.6709	3409.3418	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1613.1022	3474.2247	0.4364	0.4364
HKYI	40	-1613.5261	3475.0726	0.2856	0.7220
K2PG	37	-1623.5737	3476.5661	0.1353	0.8573
K2PI	37	-1623.7478	3476.9145	0.1137	0.9710
HKYIG	41	-1613.0067	3480.2343	0.0216	0.9926
K2PIG	38	-1623.4725	3482.5644	0.0067	0.9994
GTRI	44	-1608.0404	3488.9033	0.0003	0.9997
GTRG	44	-1608.0693	3488.9610	0.0003	0.9999
SYMI	41	-1620.0490	3494.3189	0.0000	1.0000
SYMG	41	-1620.1263	3494.4734	0.0000	1.0000
GTRIG	45	-1607.9081	3494.8391	0.0000	1.0000
HKY	39	-1627.9582	3497.7362	0.0000	1.0000
SYMIG	42	-1619.9450	3500.3115	0.0000	1.0000
K2P	36	-1638.7316	3500.6816	0.0000	1.0000
GTR	43	-1623.0528	3512.7275	0.0000	1.0000
SYM	40	-1634.9043	3517.8289	0.0000	1.0000
JC69G	36	-1655.0596	3533.3376	0.0000	1.0000
JC69I	36	-1655.1035	3533.4253	0.0000	1.0000
F81G	39	-1646.4341	3534.6880	0.0000	1.0000
F81I	39	-1646.4806	3534.7810	0.0000	1.0000
JC69IG	37	-1654.9512	3539.3212	0.0000	1.0000
F81IG	40	-1646.3253	3540.6710	0.0000	1.0000
JC69	35	-1669.6709	3556.3596	0.0000	1.0000
F81	38	-1660.8583	3557.3360	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4601.phylip = 1 - 493;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4601.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4601.phylip = 1 - 493;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4601.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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_4601.phylip = 1 - 493;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4601.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

