
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:12 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/chr1_28770.phylip" (19 taxa, 665 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1839.8668	3764.9900	0.4729	0.4729
HKYIG	41	-1839.4922	3766.5125	0.2209	0.6938
HKYI	40	-1840.6968	3766.6501	0.2062	0.9000
GTRG	44	-1837.5195	3769.4261	0.0515	0.9514
GTRIG	45	-1837.1093	3770.9068	0.0245	0.9760
GTRI	44	-1838.2817	3770.9505	0.0240	1.0000
HKY	39	-1863.1602	3809.3124	0.0000	1.0000
GTR	43	-1861.4805	3815.0545	0.0000	1.0000
K2PG	37	-1869.0763	3816.6373	0.0000	1.0000
K2PIG	38	-1868.7368	3818.2084	0.0000	1.0000
K2PI	37	-1869.9811	3818.4470	0.0000	1.0000
SYMG	41	-1868.8445	3825.2170	0.0000	1.0000
SYMIG	42	-1868.4924	3826.7919	0.0000	1.0000
SYMI	41	-1869.7420	3827.0120	0.0000	1.0000
F81G	39	-1875.2407	3833.4733	0.0000	1.0000
F81IG	40	-1874.8830	3835.0225	0.0000	1.0000
F81I	39	-1876.2759	3835.5438	0.0000	1.0000
K2P	36	-1891.3523	3858.9466	0.0000	1.0000
SYM	40	-1891.1135	3867.4833	0.0000	1.0000
JC69G	36	-1899.2379	3874.7178	0.0000	1.0000
F81	38	-1897.1037	3874.9423	0.0000	1.0000
JC69IG	37	-1898.7674	3876.0197	0.0000	1.0000
JC69I	36	-1900.1016	3876.4451	0.0000	1.0000
JC69	35	-1920.9171	3915.8406	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1839.8668	3759.7335	0.4241	0.4241
HKYIG	41	-1839.4922	3760.9844	0.2269	0.6509
HKYI	40	-1840.6968	3761.3937	0.1849	0.8358
GTRG	44	-1837.5195	3763.0390	0.0812	0.9171
GTRIG	45	-1837.1093	3764.2186	0.0450	0.9621
GTRI	44	-1838.2817	3764.5634	0.0379	1.0000
HKY	39	-1863.1602	3804.3204	0.0000	1.0000
GTR	43	-1861.4805	3808.9611	0.0000	1.0000
K2PG	37	-1869.0763	3812.1525	0.0000	1.0000
K2PIG	38	-1868.7368	3813.4736	0.0000	1.0000
K2PI	37	-1869.9811	3813.9621	0.0000	1.0000
SYMG	41	-1868.8445	3819.6889	0.0000	1.0000
SYMIG	42	-1868.4924	3820.9848	0.0000	1.0000
SYMI	41	-1869.7420	3821.4840	0.0000	1.0000
F81G	39	-1875.2407	3828.4813	0.0000	1.0000
F81IG	40	-1874.8830	3829.7661	0.0000	1.0000
F81I	39	-1876.2759	3830.5518	0.0000	1.0000
K2P	36	-1891.3523	3854.7046	0.0000	1.0000
SYM	40	-1891.1135	3862.2269	0.0000	1.0000
F81	38	-1897.1037	3870.2075	0.0000	1.0000
JC69G	36	-1899.2379	3870.4758	0.0000	1.0000
JC69IG	37	-1898.7674	3871.5349	0.0000	1.0000
JC69I	36	-1900.1016	3872.2031	0.0000	1.0000
JC69	35	-1920.9171	3911.8343	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1839.8668	3939.7250	0.6700	0.6700
HKYI	40	-1840.6968	3941.3851	0.2922	0.9622
HKYIG	41	-1839.4922	3945.4757	0.0378	1.0000
GTRG	44	-1837.5195	3961.0296	0.0000	1.0000
GTRI	44	-1838.2817	3962.5540	0.0000	1.0000
GTRIG	45	-1837.1093	3966.7090	0.0000	1.0000
K2PG	37	-1869.0763	3978.6446	0.0000	1.0000
HKY	39	-1863.1602	3979.8121	0.0000	1.0000
K2PI	37	-1869.9811	3980.4543	0.0000	1.0000
K2PIG	38	-1868.7368	3984.4655	0.0000	1.0000
GTR	43	-1861.4805	4002.4519	0.0000	1.0000
F81G	39	-1875.2407	4003.9730	0.0000	1.0000
SYMG	41	-1868.8445	4004.1802	0.0000	1.0000
SYMI	41	-1869.7420	4005.9752	0.0000	1.0000
F81I	39	-1876.2759	4006.0435	0.0000	1.0000
F81IG	40	-1874.8830	4009.7575	0.0000	1.0000
SYMIG	42	-1868.4924	4009.9759	0.0000	1.0000
K2P	36	-1891.3523	4016.6969	0.0000	1.0000
JC69G	36	-1899.2379	4032.4681	0.0000	1.0000
JC69I	36	-1900.1016	4034.1954	0.0000	1.0000
JC69IG	37	-1898.7674	4038.0270	0.0000	1.0000
F81	38	-1897.1037	4041.1994	0.0000	1.0000
SYM	40	-1891.1135	4042.2184	0.0000	1.0000
JC69	35	-1920.9171	4069.3268	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28770.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28770.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28770.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28770.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;


[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/chr1_28770.phylip = 1 - 665;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28770.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

