
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
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/chr7_2753.phylip" (19 taxa, 807 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	-3475.0087	7043.2143	0.5472	0.5472
GTRIG	45	-3474.7617	7044.9636	0.2282	0.7754
HKYG	40	-3480.8190	7045.9199	0.1415	0.9169
HKYIG	41	-3480.5039	7047.5099	0.0639	0.9807
GTRI	44	-3478.5796	7050.3560	0.0154	0.9961
HKYI	40	-3484.4224	7053.1269	0.0039	1.0000
SYMG	41	-3490.0959	7066.6938	0.0000	1.0000
SYMIG	42	-3490.1831	7069.0939	0.0000	1.0000
K2PG	37	-3495.7584	7069.1734	0.0000	1.0000
K2PIG	38	-3495.6963	7071.2521	0.0000	1.0000
SYMI	41	-3494.7683	7076.0386	0.0000	1.0000
K2PI	37	-3500.0979	7077.8526	0.0000	1.0000
GTR	43	-3554.1891	7199.3375	0.0000	1.0000
HKY	39	-3559.6246	7201.3171	0.0000	1.0000
F81G	39	-3561.9600	7205.9878	0.0000	1.0000
F81IG	40	-3561.6615	7207.6049	0.0000	1.0000
F81I	39	-3564.7364	7211.5406	0.0000	1.0000
SYM	40	-3565.0003	7214.2825	0.0000	1.0000
K2P	36	-3570.7154	7216.8906	0.0000	1.0000
JC69G	36	-3571.0496	7217.5589	0.0000	1.0000
JC69IG	37	-3570.8589	7219.3745	0.0000	1.0000
JC69I	36	-3574.1197	7223.6991	0.0000	1.0000
F81	38	-3632.5007	7344.8608	0.0000	1.0000
JC69	35	-3640.2069	7353.6824	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3475.0087	7038.0174	0.5715	0.5715
GTRIG	45	-3474.7617	7039.5234	0.2692	0.8407
HKYG	40	-3480.8190	7041.6379	0.0935	0.9342
HKYIG	41	-3480.5039	7043.0079	0.0471	0.9814
GTRI	44	-3478.5796	7045.1592	0.0161	0.9974
HKYI	40	-3484.4224	7048.8449	0.0025	1.0000
SYMG	41	-3490.0959	7062.1919	0.0000	1.0000
SYMIG	42	-3490.1831	7064.3662	0.0000	1.0000
K2PG	37	-3495.7584	7065.5167	0.0000	1.0000
K2PIG	38	-3495.6963	7067.3927	0.0000	1.0000
SYMI	41	-3494.7683	7071.5366	0.0000	1.0000
K2PI	37	-3500.0979	7074.1959	0.0000	1.0000
GTR	43	-3554.1891	7194.3781	0.0000	1.0000
HKY	39	-3559.6246	7197.2493	0.0000	1.0000
F81G	39	-3561.9600	7201.9200	0.0000	1.0000
F81IG	40	-3561.6615	7203.3229	0.0000	1.0000
F81I	39	-3564.7364	7207.4728	0.0000	1.0000
SYM	40	-3565.0003	7210.0006	0.0000	1.0000
K2P	36	-3570.7154	7213.4309	0.0000	1.0000
JC69G	36	-3571.0496	7214.0992	0.0000	1.0000
JC69IG	37	-3570.8589	7215.7178	0.0000	1.0000
JC69I	36	-3574.1197	7220.2394	0.0000	1.0000
F81	38	-3632.5007	7341.0014	0.0000	1.0000
JC69	35	-3640.2069	7350.4139	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3480.8190	7229.3709	0.9226	0.9226
HKYIG	41	-3480.5039	7235.4342	0.0445	0.9671
HKYI	40	-3484.4224	7236.5778	0.0251	0.9923
K2PG	37	-3495.7584	7239.1697	0.0069	0.9991
GTRG	44	-3475.0087	7244.5237	0.0005	0.9996
K2PIG	38	-3495.6963	7245.7390	0.0003	0.9999
K2PI	37	-3500.0979	7247.8489	0.0001	1.0000
GTRIG	45	-3474.7617	7250.7229	0.0000	1.0000
GTRI	44	-3478.5796	7251.6654	0.0000	1.0000
SYMG	41	-3490.0959	7254.6181	0.0000	1.0000
SYMIG	42	-3490.1831	7261.4858	0.0000	1.0000
SYMI	41	-3494.7683	7263.9629	0.0000	1.0000
HKY	39	-3559.6246	7380.2889	0.0000	1.0000
K2P	36	-3570.7154	7382.3905	0.0000	1.0000
JC69G	36	-3571.0496	7383.0588	0.0000	1.0000
F81G	39	-3561.9600	7384.9596	0.0000	1.0000
JC69I	36	-3574.1197	7389.1990	0.0000	1.0000
JC69IG	37	-3570.8589	7389.3708	0.0000	1.0000
F81I	39	-3564.7364	7390.5124	0.0000	1.0000
F81IG	40	-3561.6615	7391.0558	0.0000	1.0000
GTR	43	-3554.1891	7396.1911	0.0000	1.0000
SYM	40	-3565.0003	7397.7335	0.0000	1.0000
JC69	35	-3640.2069	7514.6802	0.0000	1.0000
F81	38	-3632.5007	7519.3477	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/chr7_2753.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2753.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/chr7_2753.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2753.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/chr7_2753.phylip = 1 - 807;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2753.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

