
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:48 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_10603.phylip" (19 taxa, 1013 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	-3810.9698	7716.2208	0.6370	0.6370
GTRG	44	-3813.0408	7718.1724	0.2401	0.8770
HKYIG	41	-3817.3286	7720.2040	0.0869	0.9640
HKYG	40	-3819.2953	7721.9650	0.0360	1.0000
GTRI	44	-3823.6751	7739.4411	0.0000	1.0000
HKYI	40	-3829.6425	7742.6595	0.0000	1.0000
K2PIG	38	-3836.7014	7752.4459	0.0000	1.0000
K2PG	37	-3838.6479	7754.1799	0.0000	1.0000
SYMIG	42	-3834.8272	7757.3782	0.0000	1.0000
SYMG	41	-3836.7796	7759.1061	0.0000	1.0000
K2PI	37	-3849.1694	7775.2228	0.0000	1.0000
SYMI	41	-3847.2734	7780.0936	0.0000	1.0000
F81IG	40	-3893.7696	7870.9137	0.0000	1.0000
F81G	39	-3895.2106	7871.6277	0.0000	1.0000
F81I	39	-3904.5114	7890.2294	0.0000	1.0000
JC69IG	37	-3907.6200	7892.1240	0.0000	1.0000
JC69G	36	-3909.0821	7892.8937	0.0000	1.0000
GTR	43	-3903.8206	7897.5462	0.0000	1.0000
HKY	39	-3908.3199	7897.8465	0.0000	1.0000
JC69I	36	-3918.5951	7911.9197	0.0000	1.0000
K2P	36	-3926.6652	7928.0600	0.0000	1.0000
SYM	40	-3924.9461	7933.2667	0.0000	1.0000
F81	38	-3979.5140	8038.0711	0.0000	1.0000
JC69	35	-3993.2624	8059.1041	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3810.9698	7711.9395	0.6788	0.6788
GTRG	44	-3813.0408	7714.0815	0.2326	0.9114
HKYIG	41	-3817.3286	7716.6571	0.0642	0.9756
HKYG	40	-3819.2953	7718.5905	0.0244	1.0000
GTRI	44	-3823.6751	7735.3502	0.0000	1.0000
HKYI	40	-3829.6425	7739.2850	0.0000	1.0000
K2PIG	38	-3836.7014	7749.4028	0.0000	1.0000
K2PG	37	-3838.6479	7751.2958	0.0000	1.0000
SYMIG	42	-3834.8272	7753.6545	0.0000	1.0000
SYMG	41	-3836.7796	7755.5593	0.0000	1.0000
K2PI	37	-3849.1694	7772.3387	0.0000	1.0000
SYMI	41	-3847.2734	7776.5468	0.0000	1.0000
F81IG	40	-3893.7696	7867.5393	0.0000	1.0000
F81G	39	-3895.2106	7868.4212	0.0000	1.0000
F81I	39	-3904.5114	7887.0228	0.0000	1.0000
JC69IG	37	-3907.6200	7889.2399	0.0000	1.0000
JC69G	36	-3909.0821	7890.1642	0.0000	1.0000
GTR	43	-3903.8206	7893.6412	0.0000	1.0000
HKY	39	-3908.3199	7894.6399	0.0000	1.0000
JC69I	36	-3918.5951	7909.1902	0.0000	1.0000
K2P	36	-3926.6652	7925.3305	0.0000	1.0000
SYM	40	-3924.9461	7929.8922	0.0000	1.0000
F81	38	-3979.5140	8035.0280	0.0000	1.0000
JC69	35	-3993.2624	8056.5248	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3819.2953	7915.4174	0.8161	0.8161
HKYIG	41	-3817.3286	7918.4046	0.1833	0.9993
GTRG	44	-3813.0408	7930.5911	0.0004	0.9997
K2PG	37	-3838.6479	7933.3606	0.0001	0.9998
GTRIG	45	-3810.9698	7933.3697	0.0001	1.0000
HKYI	40	-3829.6425	7936.1119	0.0000	1.0000
K2PIG	38	-3836.7014	7936.3883	0.0000	1.0000
GTRI	44	-3823.6751	7951.8598	0.0000	1.0000
K2PI	37	-3849.1694	7954.4036	0.0000	1.0000
SYMG	41	-3836.7796	7957.3068	0.0000	1.0000
SYMIG	42	-3834.8272	7960.3227	0.0000	1.0000
SYMI	41	-3847.2734	7978.2943	0.0000	1.0000
F81G	39	-3895.2106	8060.3273	0.0000	1.0000
F81IG	40	-3893.7696	8064.3661	0.0000	1.0000
JC69G	36	-3909.0821	8067.3084	0.0000	1.0000
JC69IG	37	-3907.6200	8071.3048	0.0000	1.0000
F81I	39	-3904.5114	8078.9290	0.0000	1.0000
JC69I	36	-3918.5951	8086.3344	0.0000	1.0000
HKY	39	-3908.3199	8086.5461	0.0000	1.0000
K2P	36	-3926.6652	8102.4747	0.0000	1.0000
GTR	43	-3903.8206	8105.2300	0.0000	1.0000
SYM	40	-3924.9461	8126.7191	0.0000	1.0000
F81	38	-3979.5140	8222.0135	0.0000	1.0000
JC69	35	-3993.2624	8228.7483	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/chr7_10603.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10603.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/chr7_10603.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10603.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/chr7_10603.phylip = 1 - 1013;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10603.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

