
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:34 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_8823.phylip" (19 taxa, 462 characters)

Minimum AIC  model: GTRG
Minimum AICc model: SYMG
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
SYMG	41	-1449.4972	2989.1943	0.2078	0.2078
K2PG	37	-1454.7726	2990.1773	0.1271	0.3350
GTRG	44	-1446.3478	2990.1920	0.1262	0.4611
SYMI	41	-1450.0770	2990.3540	0.1164	0.5775
SYMIG	42	-1448.9571	2990.5348	0.1063	0.6838
GTRI	44	-1446.6122	2990.7207	0.0969	0.7807
HKYG	40	-1451.6484	2991.0878	0.0806	0.8614
GTRIG	45	-1446.0869	2992.1257	0.0480	0.9093
K2PI	37	-1456.0797	2992.7915	0.0344	0.9438
HKYI	40	-1452.8521	2993.4951	0.0242	0.9679
K2PIG	38	-1455.4581	2993.9232	0.0195	0.9875
HKYIG	41	-1452.3069	2994.8139	0.0125	1.0000
K2P	36	-1481.6558	3041.5798	0.0000	1.0000
HKY	39	-1478.4021	3042.1975	0.0000	1.0000
SYM	40	-1478.0311	3043.8531	0.0000	1.0000
GTR	43	-1474.5019	3044.0565	0.0000	1.0000
JC69G	36	-1483.5696	3045.4074	0.0000	1.0000
F81G	39	-1480.2267	3045.8468	0.0000	1.0000
JC69I	36	-1484.1767	3046.6216	0.0000	1.0000
F81I	39	-1480.8936	3047.1806	0.0000	1.0000
JC69IG	37	-1483.3645	3047.3611	0.0000	1.0000
F81IG	40	-1480.1821	3048.1551	0.0000	1.0000
F81	38	-1507.0918	3097.1906	0.0000	1.0000
JC69	35	-1510.6908	3097.2971	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1446.3478	2980.6956	0.2046	0.2046
SYMG	41	-1449.4972	2980.9943	0.1762	0.3807
GTRI	44	-1446.6122	2981.2243	0.1570	0.5378
SYMIG	42	-1448.9571	2981.9142	0.1112	0.6490
SYMI	41	-1450.0770	2982.1540	0.0987	0.7476
GTRIG	45	-1446.0869	2982.1737	0.0977	0.8453
HKYG	40	-1451.6484	2983.2968	0.0557	0.9010
K2PG	37	-1454.7726	2983.5452	0.0492	0.9502
HKYI	40	-1452.8521	2985.7041	0.0167	0.9670
K2PI	37	-1456.0797	2986.1594	0.0133	0.9803
HKYIG	41	-1452.3069	2986.6139	0.0106	0.9909
K2PIG	38	-1455.4581	2986.9161	0.0091	1.0000
HKY	39	-1478.4021	3034.8041	0.0000	1.0000
GTR	43	-1474.5019	3035.0038	0.0000	1.0000
K2P	36	-1481.6558	3035.3116	0.0000	1.0000
SYM	40	-1478.0311	3036.0621	0.0000	1.0000
F81G	39	-1480.2267	3038.4534	0.0000	1.0000
JC69G	36	-1483.5696	3039.1392	0.0000	1.0000
F81I	39	-1480.8936	3039.7873	0.0000	1.0000
JC69I	36	-1484.1767	3040.3534	0.0000	1.0000
F81IG	40	-1480.1821	3040.3641	0.0000	1.0000
JC69IG	37	-1483.3645	3040.7290	0.0000	1.0000
F81	38	-1507.0918	3090.1835	0.0000	1.0000
JC69	35	-1510.6908	3091.3816	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1454.7726	3136.5611	0.7701	0.7701
K2PI	37	-1456.0797	3139.1753	0.2084	0.9785
K2PIG	38	-1455.4581	3144.0676	0.0181	0.9965
HKYG	40	-1451.6484	3148.7194	0.0018	0.9983
SYMG	41	-1449.4972	3150.5525	0.0007	0.9990
HKYI	40	-1452.8521	3151.1267	0.0005	0.9995
SYMI	41	-1450.0770	3151.7122	0.0004	0.9999
SYMIG	42	-1448.9571	3155.6080	0.0001	1.0000
HKYIG	41	-1452.3069	3156.1720	0.0000	1.0000
GTRG	44	-1446.3478	3162.6605	0.0000	1.0000
GTRI	44	-1446.6122	3163.1892	0.0000	1.0000
GTRIG	45	-1446.0869	3168.2742	0.0000	1.0000
K2P	36	-1481.6558	3184.1919	0.0000	1.0000
JC69G	36	-1483.5696	3188.0195	0.0000	1.0000
JC69I	36	-1484.1767	3189.2337	0.0000	1.0000
JC69IG	37	-1483.3645	3193.7449	0.0000	1.0000
HKY	39	-1478.4021	3196.0912	0.0000	1.0000
F81G	39	-1480.2267	3199.7405	0.0000	1.0000
F81I	39	-1480.8936	3201.0743	0.0000	1.0000
SYM	40	-1478.0311	3201.4847	0.0000	1.0000
F81IG	40	-1480.1821	3205.7867	0.0000	1.0000
GTR	43	-1474.5019	3212.8331	0.0000	1.0000
JC69	35	-1510.6908	3236.1264	0.0000	1.0000
F81	38	-1507.0918	3247.3350	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/chr6_8823.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8823.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 (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8823.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8823.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=Fixed(Equal);
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/chr6_8823.phylip = 1 - 462;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8823.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

