
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:51 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/chr2_23138.phylip" (19 taxa, 969 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2664.7003	5412.9350	0.5030	0.5030
HKYI	40	-2665.5823	5414.6991	0.2082	0.7112
HKYIG	41	-2664.5463	5414.8079	0.1972	0.9084
GTRG	44	-2662.5626	5417.4110	0.0537	0.9621
GTRIG	45	-2662.2879	5419.0611	0.0235	0.9856
GTRI	44	-2663.8776	5420.0409	0.0144	1.0000
HKY	39	-2690.0575	5461.4735	0.0000	1.0000
GTR	43	-2689.6596	5469.4100	0.0000	1.0000
K2PG	37	-2705.3343	5487.6891	0.0000	1.0000
K2PI	37	-2706.1630	5489.3464	0.0000	1.0000
K2PIG	38	-2705.2024	5489.5919	0.0000	1.0000
F81G	39	-2708.2931	5497.9445	0.0000	1.0000
SYMG	41	-2706.3811	5498.4775	0.0000	1.0000
F81I	39	-2708.8541	5499.0667	0.0000	1.0000
F81IG	40	-2708.1852	5499.9049	0.0000	1.0000
SYMIG	42	-2706.2150	5500.3306	0.0000	1.0000
SYMI	41	-2707.3759	5500.4670	0.0000	1.0000
K2P	36	-2729.8788	5534.6160	0.0000	1.0000
SYM	40	-2731.5882	5546.7108	0.0000	1.0000
F81	38	-2735.3244	5549.8358	0.0000	1.0000
JC69G	36	-2742.5217	5559.9018	0.0000	1.0000
JC69I	36	-2743.0147	5560.8878	0.0000	1.0000
JC69IG	37	-2742.4506	5561.9215	0.0000	1.0000
JC69	35	-2769.2281	5611.1571	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2664.7003	5409.4005	0.4728	0.4728
HKYIG	41	-2664.5463	5411.0927	0.2029	0.6756
HKYI	40	-2665.5823	5411.1646	0.1957	0.8713
GTRG	44	-2662.5626	5413.1253	0.0734	0.9447
GTRIG	45	-2662.2879	5414.5758	0.0356	0.9803
GTRI	44	-2663.8776	5415.7552	0.0197	1.0000
HKY	39	-2690.0575	5458.1150	0.0000	1.0000
GTR	43	-2689.6596	5465.3191	0.0000	1.0000
K2PG	37	-2705.3343	5484.6687	0.0000	1.0000
K2PI	37	-2706.1630	5486.3260	0.0000	1.0000
K2PIG	38	-2705.2024	5486.4048	0.0000	1.0000
F81G	39	-2708.2931	5494.5861	0.0000	1.0000
SYMG	41	-2706.3811	5494.7623	0.0000	1.0000
F81I	39	-2708.8541	5495.7083	0.0000	1.0000
F81IG	40	-2708.1852	5496.3704	0.0000	1.0000
SYMIG	42	-2706.2150	5496.4299	0.0000	1.0000
SYMI	41	-2707.3759	5496.7518	0.0000	1.0000
K2P	36	-2729.8788	5531.7576	0.0000	1.0000
SYM	40	-2731.5882	5543.1763	0.0000	1.0000
F81	38	-2735.3244	5546.6487	0.0000	1.0000
JC69G	36	-2742.5217	5557.0434	0.0000	1.0000
JC69I	36	-2743.0147	5558.0294	0.0000	1.0000
JC69IG	37	-2742.4506	5558.9011	0.0000	1.0000
JC69	35	-2769.2281	5608.4561	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2664.7003	5604.4511	0.6890	0.6890
HKYI	40	-2665.5823	5606.2152	0.2852	0.9742
HKYIG	41	-2664.5463	5611.0195	0.0258	1.0000
GTRG	44	-2662.5626	5627.6809	0.0000	1.0000
GTRI	44	-2663.8776	5630.3108	0.0000	1.0000
GTRIG	45	-2662.2879	5634.0077	0.0000	1.0000
HKY	39	-2690.0575	5648.2893	0.0000	1.0000
K2PG	37	-2705.3343	5665.0905	0.0000	1.0000
K2PI	37	-2706.1630	5666.7478	0.0000	1.0000
K2PIG	38	-2705.2024	5671.7029	0.0000	1.0000
GTR	43	-2689.6596	5674.9985	0.0000	1.0000
F81G	39	-2708.2931	5684.7604	0.0000	1.0000
F81I	39	-2708.8541	5685.8826	0.0000	1.0000
F81IG	40	-2708.1852	5691.4210	0.0000	1.0000
SYMG	41	-2706.3811	5694.6891	0.0000	1.0000
SYMI	41	-2707.3759	5696.6786	0.0000	1.0000
SYMIG	42	-2706.2150	5701.2331	0.0000	1.0000
K2P	36	-2729.8788	5707.3032	0.0000	1.0000
F81	38	-2735.3244	5731.9468	0.0000	1.0000
JC69G	36	-2742.5217	5732.5889	0.0000	1.0000
JC69I	36	-2743.0147	5733.5749	0.0000	1.0000
SYM	40	-2731.5882	5738.2269	0.0000	1.0000
JC69IG	37	-2742.4506	5739.3229	0.0000	1.0000
JC69	35	-2769.2281	5779.1254	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23138.phylip = 1 - 969;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23138.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;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23138.phylip = 1 - 969;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23138.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;


[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/chr2_23138.phylip = 1 - 969;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23138.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

