
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:37 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/chr4_7258.phylip" (19 taxa, 457 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	-2100.9137	4289.7121	0.6911	0.6911
GTRG	44	-2097.3212	4292.2540	0.1939	0.8850
HKYIG	41	-2101.7198	4293.7385	0.0923	0.9773
GTRIG	45	-2098.3915	4296.8561	0.0194	0.9968
K2PG	37	-2110.4743	4301.6598	0.0018	0.9985
K2PIG	38	-2109.8744	4302.8398	0.0010	0.9995
HKYI	40	-2108.7790	4305.4427	0.0003	0.9997
SYMIG	42	-2107.1872	4307.0990	0.0001	0.9999
SYMG	41	-2108.7467	4307.7922	0.0001	0.9999
GTRI	44	-2105.5624	4308.7364	0.0001	1.0000
K2PI	37	-2117.2288	4315.1689	0.0000	1.0000
SYMI	41	-2116.0763	4322.4513	0.0000	1.0000
HKY	39	-2158.8161	4403.1142	0.0000	1.0000
GTR	43	-2155.5535	4406.2692	0.0000	1.0000
F81G	39	-2161.4513	4408.3847	0.0000	1.0000
F81IG	40	-2160.9302	4409.7449	0.0000	1.0000
K2P	36	-2167.7495	4413.8420	0.0000	1.0000
JC69G	36	-2170.2105	4418.7639	0.0000	1.0000
SYM	40	-2166.0189	4419.9225	0.0000	1.0000
JC69IG	37	-2169.6781	4420.0675	0.0000	1.0000
F81I	39	-2167.8533	4421.1886	0.0000	1.0000
JC69I	36	-2176.4332	4431.2092	0.0000	1.0000
F81	38	-2216.6445	4516.3800	0.0000	1.0000
JC69	35	-2225.8320	4527.6498	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2100.9137	4281.8275	0.5217	0.5217
GTRG	44	-2097.3212	4282.6423	0.3471	0.8688
HKYIG	41	-2101.7198	4285.4397	0.0857	0.9545
GTRIG	45	-2098.3915	4286.7831	0.0438	0.9983
K2PG	37	-2110.4743	4294.9485	0.0007	0.9990
K2PIG	38	-2109.8744	4295.7489	0.0005	0.9995
HKYI	40	-2108.7790	4297.5580	0.0002	0.9997
SYMIG	42	-2107.1872	4298.3744	0.0001	0.9998
GTRI	44	-2105.5624	4299.1248	0.0001	0.9999
SYMG	41	-2108.7467	4299.4934	0.0001	1.0000
K2PI	37	-2117.2288	4308.4577	0.0000	1.0000
SYMI	41	-2116.0763	4314.1525	0.0000	1.0000
HKY	39	-2158.8161	4395.6321	0.0000	1.0000
GTR	43	-2155.5535	4397.1070	0.0000	1.0000
F81G	39	-2161.4513	4400.9027	0.0000	1.0000
F81IG	40	-2160.9302	4401.8603	0.0000	1.0000
K2P	36	-2167.7495	4407.4991	0.0000	1.0000
SYM	40	-2166.0189	4412.0379	0.0000	1.0000
JC69G	36	-2170.2105	4412.4210	0.0000	1.0000
JC69IG	37	-2169.6781	4413.3563	0.0000	1.0000
F81I	39	-2167.8533	4413.7066	0.0000	1.0000
JC69I	36	-2176.4332	4424.8664	0.0000	1.0000
F81	38	-2216.6445	4509.2891	0.0000	1.0000
JC69	35	-2225.8320	4521.6640	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2100.9137	4446.8148	0.5652	0.5652
K2PG	37	-2110.4743	4447.5618	0.3890	0.9543
K2PIG	38	-2109.8744	4452.4869	0.0332	0.9874
HKYIG	41	-2101.7198	4454.5517	0.0118	0.9992
K2PI	37	-2117.2288	4461.0710	0.0005	0.9997
HKYI	40	-2108.7790	4462.5454	0.0002	0.9999
GTRG	44	-2097.3212	4464.1284	0.0001	1.0000
SYMG	41	-2108.7467	4468.6055	0.0000	1.0000
SYMIG	42	-2107.1872	4471.6111	0.0000	1.0000
GTRIG	45	-2098.3915	4472.3938	0.0000	1.0000
GTRI	44	-2105.5624	4480.6108	0.0000	1.0000
SYMI	41	-2116.0763	4483.2645	0.0000	1.0000
K2P	36	-2167.7495	4555.9877	0.0000	1.0000
HKY	39	-2158.8161	4556.4948	0.0000	1.0000
JC69G	36	-2170.2105	4560.9096	0.0000	1.0000
F81G	39	-2161.4513	4561.7654	0.0000	1.0000
JC69IG	37	-2169.6781	4565.9696	0.0000	1.0000
F81IG	40	-2160.9302	4566.8477	0.0000	1.0000
JC69I	36	-2176.4332	4573.3550	0.0000	1.0000
GTR	43	-2155.5535	4574.4684	0.0000	1.0000
F81I	39	-2167.8533	4574.5693	0.0000	1.0000
SYM	40	-2166.0189	4577.0252	0.0000	1.0000
F81	38	-2216.6445	4666.0270	0.0000	1.0000
JC69	35	-2225.8320	4666.0280	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/chr4_7258.phylip = 1 - 457;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7258.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/chr4_7258.phylip = 1 - 457;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7258.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/chr4_7258.phylip = 1 - 457;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7258.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

