
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:21 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/chr5_1684.phylip" (19 taxa, 854 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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
GTRIG	45	-3978.9338	8052.9913	0.9716	0.9716
GTRI	44	-3984.1360	8061.1669	0.0163	0.9879
HKYIG	41	-3988.4956	8063.2326	0.0058	0.9937
HKYI	40	-3990.1419	8064.3182	0.0034	0.9971
GTRG	44	-3986.3807	8065.6563	0.0017	0.9988
HKYG	40	-3991.1761	8066.3866	0.0012	1.0000
K2PIG	38	-4002.8011	8085.2389	0.0000	1.0000
SYMIG	42	-3998.5174	8085.4887	0.0000	1.0000
SYMI	41	-4000.0100	8086.2613	0.0000	1.0000
K2PI	37	-4004.4634	8086.3729	0.0000	1.0000
K2PG	37	-4005.2203	8087.8866	0.0000	1.0000
SYMG	41	-4001.1258	8088.4930	0.0000	1.0000
HKY	39	-4067.2316	8216.2961	0.0000	1.0000
GTR	43	-4067.7790	8226.2297	0.0000	1.0000
K2P	36	-4078.6788	8232.6183	0.0000	1.0000
SYM	40	-4082.1638	8248.3621	0.0000	1.0000
F81IG	40	-4088.3804	8260.7952	0.0000	1.0000
F81I	39	-4089.6651	8261.1632	0.0000	1.0000
F81G	39	-4091.1833	8264.1994	0.0000	1.0000
JC69IG	37	-4098.8989	8275.2438	0.0000	1.0000
JC69I	36	-4100.2740	8275.8088	0.0000	1.0000
JC69G	36	-4101.5450	8278.3508	0.0000	1.0000
F81	38	-4161.9936	8403.6240	0.0000	1.0000
JC69	35	-4171.1110	8415.3026	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3978.9338	8047.8675	0.9774	0.9774
GTRI	44	-3984.1360	8056.2720	0.0146	0.9920
HKYIG	41	-3988.4956	8058.9912	0.0038	0.9958
HKYI	40	-3990.1419	8060.2838	0.0020	0.9978
GTRG	44	-3986.3807	8060.7614	0.0015	0.9993
HKYG	40	-3991.1761	8062.3522	0.0007	1.0000
SYMIG	42	-3998.5174	8081.0349	0.0000	1.0000
K2PIG	38	-4002.8011	8081.6021	0.0000	1.0000
SYMI	41	-4000.0100	8082.0199	0.0000	1.0000
K2PI	37	-4004.4634	8082.9269	0.0000	1.0000
SYMG	41	-4001.1258	8084.2516	0.0000	1.0000
K2PG	37	-4005.2203	8084.4406	0.0000	1.0000
HKY	39	-4067.2316	8212.4631	0.0000	1.0000
GTR	43	-4067.7790	8221.5581	0.0000	1.0000
K2P	36	-4078.6788	8229.3576	0.0000	1.0000
SYM	40	-4082.1638	8244.3277	0.0000	1.0000
F81IG	40	-4088.3804	8256.7607	0.0000	1.0000
F81I	39	-4089.6651	8257.3303	0.0000	1.0000
F81G	39	-4091.1833	8260.3665	0.0000	1.0000
JC69IG	37	-4098.8989	8271.7978	0.0000	1.0000
JC69I	36	-4100.2740	8272.5481	0.0000	1.0000
JC69G	36	-4101.5450	8275.0901	0.0000	1.0000
F81	38	-4161.9936	8399.9872	0.0000	1.0000
JC69	35	-4171.1110	8412.2219	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-3990.1419	8250.2810	0.6402	0.6402
HKYG	40	-3991.1761	8252.3494	0.2276	0.8678
HKYIG	41	-3988.4956	8253.7384	0.1137	0.9815
K2PI	37	-4004.4634	8258.6743	0.0096	0.9911
K2PG	37	-4005.2203	8260.1880	0.0045	0.9957
GTRIG	45	-3978.9338	8261.6144	0.0022	0.9979
K2PIG	38	-4002.8011	8262.0995	0.0017	0.9996
GTRI	44	-3984.1360	8265.2690	0.0004	1.0000
GTRG	44	-3986.3807	8269.7583	0.0000	1.0000
SYMI	41	-4000.0100	8276.7671	0.0000	1.0000
SYMG	41	-4001.1258	8278.9988	0.0000	1.0000
SYMIG	42	-3998.5174	8280.5320	0.0000	1.0000
HKY	39	-4067.2316	8397.7105	0.0000	1.0000
K2P	36	-4078.6788	8400.3551	0.0000	1.0000
GTR	43	-4067.7790	8425.8051	0.0000	1.0000
SYM	40	-4082.1638	8434.3249	0.0000	1.0000
F81I	39	-4089.6651	8442.5776	0.0000	1.0000
JC69I	36	-4100.2740	8443.5456	0.0000	1.0000
F81G	39	-4091.1833	8445.6138	0.0000	1.0000
JC69G	36	-4101.5450	8446.0876	0.0000	1.0000
F81IG	40	-4088.3804	8446.7580	0.0000	1.0000
JC69IG	37	-4098.8989	8447.5452	0.0000	1.0000
JC69	35	-4171.1110	8578.4695	0.0000	1.0000
F81	38	-4161.9936	8580.4846	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip = 1 - 854;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip = 1 - 854;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip = 1 - 854;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1684.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

