
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:03 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/chr8_4947.phylip" (19 taxa, 574 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1974.2464	4043.9787	0.5877	0.5877
GTRIG	45	-1974.1297	4046.1002	0.2035	0.7912
GTRI	44	-1976.1114	4047.7087	0.0910	0.8822
HKYG	40	-1980.7901	4047.7340	0.0899	0.9721
HKYIG	41	-1981.2171	4050.9079	0.0184	0.9905
HKYI	40	-1983.0387	4052.2312	0.0095	1.0000
SYMG	41	-1996.5030	4081.4798	0.0000	1.0000
SYMIG	42	-1995.8521	4082.5065	0.0000	1.0000
K2PG	37	-2002.0770	4083.4002	0.0000	1.0000
SYMI	41	-1997.9317	4084.3371	0.0000	1.0000
GTR	43	-1995.9844	4085.1085	0.0000	1.0000
K2PIG	38	-2001.9503	4085.4408	0.0000	1.0000
K2PI	37	-2004.2872	4087.8207	0.0000	1.0000
HKY	39	-2002.7020	4089.2468	0.0000	1.0000
SYM	40	-2017.7127	4121.5792	0.0000	1.0000
K2P	36	-2024.0581	4125.0771	0.0000	1.0000
F81G	39	-2044.9519	4173.7465	0.0000	1.0000
F81IG	40	-2044.9242	4176.0022	0.0000	1.0000
F81I	39	-2047.0978	4178.0382	0.0000	1.0000
JC69G	36	-2061.3602	4199.6813	0.0000	1.0000
JC69IG	37	-2061.3214	4201.8890	0.0000	1.0000
JC69I	36	-2063.6703	4204.3016	0.0000	1.0000
F81	38	-2067.3879	4216.3161	0.0000	1.0000
JC69	35	-2083.5128	4241.7096	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1974.2464	4036.4929	0.5973	0.5973
GTRIG	45	-1974.1297	4038.2593	0.2470	0.8443
GTRI	44	-1976.1114	4040.2229	0.0925	0.9368
HKYG	40	-1980.7901	4041.5802	0.0469	0.9838
HKYIG	41	-1981.2171	4044.4342	0.0113	0.9950
HKYI	40	-1983.0387	4046.0773	0.0050	1.0000
SYMG	41	-1996.5030	4075.0061	0.0000	1.0000
SYMIG	42	-1995.8521	4075.7042	0.0000	1.0000
SYMI	41	-1997.9317	4077.8635	0.0000	1.0000
GTR	43	-1995.9844	4077.9688	0.0000	1.0000
K2PG	37	-2002.0770	4078.1540	0.0000	1.0000
K2PIG	38	-2001.9503	4079.9006	0.0000	1.0000
K2PI	37	-2004.2872	4082.5744	0.0000	1.0000
HKY	39	-2002.7020	4083.4041	0.0000	1.0000
SYM	40	-2017.7127	4115.4253	0.0000	1.0000
K2P	36	-2024.0581	4120.1162	0.0000	1.0000
F81G	39	-2044.9519	4167.9038	0.0000	1.0000
F81IG	40	-2044.9242	4169.8484	0.0000	1.0000
F81I	39	-2047.0978	4172.1955	0.0000	1.0000
JC69G	36	-2061.3602	4194.7204	0.0000	1.0000
JC69IG	37	-2061.3214	4196.6427	0.0000	1.0000
JC69I	36	-2063.6703	4199.3407	0.0000	1.0000
F81	38	-2067.3879	4210.7759	0.0000	1.0000
JC69	35	-2083.5128	4237.0255	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1980.7901	4215.6854	0.8808	0.8808
HKYI	40	-1983.0387	4220.1825	0.0930	0.9738
HKYIG	41	-1981.2171	4222.8920	0.0240	0.9978
GTRG	44	-1974.2464	4228.0086	0.0019	0.9996
GTRI	44	-1976.1114	4231.7386	0.0003	0.9999
GTRIG	45	-1974.1297	4234.1277	0.0001	1.0000
K2PG	37	-2002.0770	4239.2012	0.0000	1.0000
K2PI	37	-2004.2872	4243.6217	0.0000	1.0000
K2PIG	38	-2001.9503	4245.3005	0.0000	1.0000
HKY	39	-2002.7020	4253.1566	0.0000	1.0000
SYMG	41	-1996.5030	4253.4639	0.0000	1.0000
SYMI	41	-1997.9317	4256.3213	0.0000	1.0000
SYMIG	42	-1995.8521	4258.5147	0.0000	1.0000
GTR	43	-1995.9844	4265.1319	0.0000	1.0000
K2P	36	-2024.0581	4276.8108	0.0000	1.0000
SYM	40	-2017.7127	4289.5305	0.0000	1.0000
F81G	39	-2044.9519	4337.6563	0.0000	1.0000
F81I	39	-2047.0978	4341.9481	0.0000	1.0000
F81IG	40	-2044.9242	4343.9535	0.0000	1.0000
JC69G	36	-2061.3602	4351.4150	0.0000	1.0000
JC69I	36	-2063.6703	4356.0354	0.0000	1.0000
JC69IG	37	-2061.3214	4357.6900	0.0000	1.0000
F81	38	-2067.3879	4376.1758	0.0000	1.0000
JC69	35	-2083.5128	4389.3676	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/chr8_4947.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4947.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/chr8_4947.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4947.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4947.phylip = 1 - 574;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4947.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

