
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:13 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/chr3_21776.phylip" (19 taxa, 553 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-2093.8292	4283.4536	0.4168	0.4168
SYMG	41	-2097.8104	4284.3606	0.2648	0.6816
GTRIG	45	-2093.5656	4285.2968	0.1658	0.8474
SYMIG	42	-2097.5762	4286.2348	0.1037	0.9512
GTRI	44	-2096.7754	4289.3460	0.0219	0.9731
SYMI	41	-2100.3284	4289.3966	0.0214	0.9944
K2PG	37	-2106.9583	4293.3767	0.0029	0.9974
K2PIG	38	-2106.7619	4295.2903	0.0011	0.9985
HKYG	40	-2104.7255	4295.8573	0.0008	0.9993
HKYIG	41	-2104.5233	4297.7862	0.0003	0.9996
K2PI	37	-2109.3137	4298.0876	0.0003	0.9999
HKYI	40	-2107.1098	4300.6259	0.0001	1.0000
SYM	40	-2146.6209	4379.6481	0.0000	1.0000
GTR	43	-2143.6422	4380.7185	0.0000	1.0000
K2P	36	-2152.8947	4382.9522	0.0000	1.0000
HKY	39	-2151.1366	4386.3550	0.0000	1.0000
F81IG	40	-2163.6007	4413.6076	0.0000	1.0000
JC69G	36	-2168.6426	4414.4479	0.0000	1.0000
JC69IG	37	-2168.3905	4416.2411	0.0000	1.0000
F81G	39	-2166.9740	4418.0299	0.0000	1.0000
JC69I	36	-2171.6120	4420.3867	0.0000	1.0000
F81I	39	-2169.9827	4424.0473	0.0000	1.0000
JC69	35	-2209.9558	4494.7859	0.0000	1.0000
F81	38	-2208.3666	4498.4998	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2093.8292	4275.6583	0.4727	0.4727
GTRIG	45	-2093.5656	4277.1312	0.2263	0.6990
SYMG	41	-2097.8104	4277.6209	0.1772	0.8762
SYMIG	42	-2097.5762	4279.1524	0.0824	0.9586
GTRI	44	-2096.7754	4281.5507	0.0248	0.9834
SYMI	41	-2100.3284	4282.6569	0.0143	0.9977
K2PG	37	-2106.9583	4287.9165	0.0010	0.9987
HKYG	40	-2104.7255	4289.4511	0.0005	0.9992
K2PIG	38	-2106.7619	4289.5237	0.0005	0.9996
HKYIG	41	-2104.5233	4291.0465	0.0002	0.9999
K2PI	37	-2109.3137	4292.6274	0.0001	1.0000
HKYI	40	-2107.1098	4294.2197	0.0000	1.0000
SYM	40	-2146.6209	4373.2419	0.0000	1.0000
GTR	43	-2143.6422	4373.2843	0.0000	1.0000
K2P	36	-2152.8947	4377.7894	0.0000	1.0000
HKY	39	-2151.1366	4380.2731	0.0000	1.0000
F81IG	40	-2163.6007	4407.2013	0.0000	1.0000
JC69G	36	-2168.6426	4409.2851	0.0000	1.0000
JC69IG	37	-2168.3905	4410.7809	0.0000	1.0000
F81G	39	-2166.9740	4411.9481	0.0000	1.0000
JC69I	36	-2171.6120	4415.2239	0.0000	1.0000
F81I	39	-2169.9827	4417.9654	0.0000	1.0000
JC69	35	-2209.9558	4489.9116	0.0000	1.0000
F81	38	-2208.3666	4492.7333	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2106.9583	4447.5848	0.8457	0.8457
K2PI	37	-2109.3137	4452.2957	0.0802	0.9259
K2PIG	38	-2106.7619	4453.5073	0.0438	0.9697
SYMG	41	-2097.8104	4454.5506	0.0260	0.9957
SYMI	41	-2100.3284	4459.5866	0.0021	0.9978
SYMIG	42	-2097.5762	4460.3975	0.0014	0.9992
HKYG	40	-2104.7255	4462.0654	0.0006	0.9998
GTRG	44	-2093.8292	4465.5341	0.0001	0.9999
HKYI	40	-2107.1098	4466.8340	0.0001	1.0000
HKYIG	41	-2104.5233	4467.9762	0.0000	1.0000
GTRIG	45	-2093.5656	4471.3223	0.0000	1.0000
GTRI	44	-2096.7754	4471.4265	0.0000	1.0000
K2P	36	-2152.8947	4533.1423	0.0000	1.0000
SYM	40	-2146.6209	4545.8562	0.0000	1.0000
HKY	39	-2151.1366	4548.5721	0.0000	1.0000
GTR	43	-2143.6422	4558.8447	0.0000	1.0000
JC69G	36	-2168.6426	4564.6380	0.0000	1.0000
JC69IG	37	-2168.3905	4570.4492	0.0000	1.0000
JC69I	36	-2171.6120	4570.5768	0.0000	1.0000
F81IG	40	-2163.6007	4579.8157	0.0000	1.0000
F81G	39	-2166.9740	4580.2470	0.0000	1.0000
F81I	39	-2169.9827	4586.2644	0.0000	1.0000
JC69	35	-2209.9558	4640.9492	0.0000	1.0000
F81	38	-2208.3666	4656.7169	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/chr3_21776.phylip = 1 - 553;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21776.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/chr3_21776.phylip = 1 - 553;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21776.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21776.phylip = 1 - 553;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_21776.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

