
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:22 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/chr6_3100.phylip" (19 taxa, 774 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2426.7432	4949.1732	0.6022	0.6022
GTRG	44	-2428.3006	4950.0333	0.3917	0.9940
GTRI	44	-2432.8435	4959.1192	0.0042	0.9981
HKYG	40	-2438.7758	4962.0263	0.0010	0.9991
HKYIG	41	-2437.8569	4962.4188	0.0008	0.9999
HKYI	40	-2441.0465	4966.5678	0.0001	1.0000
SYMG	41	-2452.8001	4992.3052	0.0000	1.0000
SYMIG	42	-2452.0839	4993.1091	0.0000	1.0000
K2PG	37	-2457.9610	4993.7426	0.0000	1.0000
K2PIG	38	-2457.5002	4995.0331	0.0000	1.0000
SYMI	41	-2454.5927	4995.8904	0.0000	1.0000
K2PI	37	-2459.2831	4996.3869	0.0000	1.0000
F81G	39	-2481.4465	5045.1436	0.0000	1.0000
F81IG	40	-2480.9076	5046.2900	0.0000	1.0000
F81I	39	-2482.9761	5048.2029	0.0000	1.0000
JC69G	36	-2497.1590	5069.9327	0.0000	1.0000
JC69IG	37	-2496.7361	5071.2929	0.0000	1.0000
JC69I	36	-2498.4545	5072.5238	0.0000	1.0000
GTR	43	-2493.9506	5079.0848	0.0000	1.0000
HKY	39	-2502.8579	5087.9665	0.0000	1.0000
SYM	40	-2518.2381	5120.9510	0.0000	1.0000
K2P	36	-2523.1842	5121.9830	0.0000	1.0000
F81	38	-2544.5818	5169.1963	0.0000	1.0000
JC69	35	-2560.8477	5195.1099	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2426.7432	4943.4864	0.6327	0.6327
GTRG	44	-2428.3006	4944.6012	0.3623	0.9950
GTRI	44	-2432.8435	4953.6871	0.0039	0.9989
HKYG	40	-2438.7758	4957.5515	0.0006	0.9994
HKYIG	41	-2437.8569	4957.7139	0.0005	0.9999
HKYI	40	-2441.0465	4962.0930	0.0001	1.0000
SYMG	41	-2452.8001	4987.6002	0.0000	1.0000
SYMIG	42	-2452.0839	4988.1679	0.0000	1.0000
K2PG	37	-2457.9610	4989.9219	0.0000	1.0000
K2PIG	38	-2457.5002	4991.0004	0.0000	1.0000
SYMI	41	-2454.5927	4991.1854	0.0000	1.0000
K2PI	37	-2459.2831	4992.5662	0.0000	1.0000
F81G	39	-2481.4465	5040.8929	0.0000	1.0000
F81IG	40	-2480.9076	5041.8153	0.0000	1.0000
F81I	39	-2482.9761	5043.9522	0.0000	1.0000
JC69G	36	-2497.1590	5066.3180	0.0000	1.0000
JC69IG	37	-2496.7361	5067.4722	0.0000	1.0000
JC69I	36	-2498.4545	5068.9091	0.0000	1.0000
GTR	43	-2493.9506	5073.9013	0.0000	1.0000
HKY	39	-2502.8579	5083.7158	0.0000	1.0000
SYM	40	-2518.2381	5116.4762	0.0000	1.0000
K2P	36	-2523.1842	5118.3684	0.0000	1.0000
F81	38	-2544.5818	5165.1636	0.0000	1.0000
JC69	35	-2560.8477	5191.6953	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2438.7758	5143.6144	0.7916	0.7916
HKYI	40	-2441.0465	5148.1559	0.0817	0.8733
HKYIG	41	-2437.8569	5148.4283	0.0713	0.9446
GTRG	44	-2428.3006	5149.2703	0.0468	0.9914
GTRIG	45	-2426.7432	5152.8071	0.0080	0.9994
GTRI	44	-2432.8435	5158.3562	0.0005	0.9999
K2PG	37	-2457.9610	5162.0301	0.0001	1.0000
K2PI	37	-2459.2831	5164.6744	0.0000	1.0000
K2PIG	38	-2457.5002	5167.7601	0.0000	1.0000
SYMG	41	-2452.8001	5178.3147	0.0000	1.0000
SYMI	41	-2454.5927	5181.8999	0.0000	1.0000
SYMIG	42	-2452.0839	5183.5339	0.0000	1.0000
F81G	39	-2481.4465	5222.3042	0.0000	1.0000
F81I	39	-2482.9761	5225.3635	0.0000	1.0000
F81IG	40	-2480.9076	5227.8782	0.0000	1.0000
JC69G	36	-2497.1590	5233.7746	0.0000	1.0000
JC69I	36	-2498.4545	5236.3657	0.0000	1.0000
JC69IG	37	-2496.7361	5239.5804	0.0000	1.0000
HKY	39	-2502.8579	5265.1271	0.0000	1.0000
GTR	43	-2493.9506	5273.9189	0.0000	1.0000
K2P	36	-2523.1842	5285.8250	0.0000	1.0000
SYM	40	-2518.2381	5302.5391	0.0000	1.0000
F81	38	-2544.5818	5341.9234	0.0000	1.0000
JC69	35	-2560.8477	5354.5003	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/chr6_3100.phylip = 1 - 774;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3100.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/chr6_3100.phylip = 1 - 774;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3100.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3100.phylip = 1 - 774;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3100.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

