
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:33 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_8822.phylip" (19 taxa, 730 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-2740.9572	5575.6954	0.5446	0.5446
GTRIG	45	-2740.0006	5576.0539	0.4552	0.9999
GTRI	44	-2749.3252	5592.4314	0.0001	1.0000
HKYIG	41	-2758.4731	5603.9519	0.0000	1.0000
HKYG	40	-2759.6440	5604.0484	0.0000	1.0000
HKYI	40	-2766.9829	5618.7263	0.0000	1.0000
SYMIG	42	-2773.4071	5636.0719	0.0000	1.0000
SYMG	41	-2774.7697	5636.5452	0.0000	1.0000
K2PIG	38	-2781.7856	5643.8607	0.0000	1.0000
K2PG	37	-2783.0939	5644.2514	0.0000	1.0000
SYMI	41	-2781.6660	5650.3378	0.0000	1.0000
K2PI	37	-2790.2368	5658.5372	0.0000	1.0000
GTR	43	-2803.8120	5699.1400	0.0000	1.0000
HKY	39	-2821.4339	5725.3896	0.0000	1.0000
F81IG	40	-2829.0067	5742.7740	0.0000	1.0000
F81G	39	-2830.3370	5743.1958	0.0000	1.0000
F81I	39	-2837.1254	5756.7725	0.0000	1.0000
SYM	40	-2838.7779	5762.3164	0.0000	1.0000
K2P	36	-2847.6069	5771.0580	0.0000	1.0000
JC69IG	37	-2847.1189	5772.3013	0.0000	1.0000
JC69G	36	-2848.4739	5772.7920	0.0000	1.0000
JC69I	36	-2855.1965	5786.2372	0.0000	1.0000
F81	38	-2891.2177	5862.7248	0.0000	1.0000
JC69	35	-2910.8314	5895.2939	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2740.9572	5569.9143	0.5108	0.5108
GTRIG	45	-2740.0006	5570.0013	0.4891	0.9999
GTRI	44	-2749.3252	5586.6504	0.0001	1.0000
HKYIG	41	-2758.4731	5598.9461	0.0000	1.0000
HKYG	40	-2759.6440	5599.2879	0.0000	1.0000
HKYI	40	-2766.9829	5613.9658	0.0000	1.0000
SYMIG	42	-2773.4071	5630.8143	0.0000	1.0000
SYMG	41	-2774.7697	5631.5394	0.0000	1.0000
K2PIG	38	-2781.7856	5639.5713	0.0000	1.0000
K2PG	37	-2783.0939	5640.1878	0.0000	1.0000
SYMI	41	-2781.6660	5645.3320	0.0000	1.0000
K2PI	37	-2790.2368	5654.4736	0.0000	1.0000
GTR	43	-2803.8120	5693.6239	0.0000	1.0000
HKY	39	-2821.4339	5720.8678	0.0000	1.0000
F81IG	40	-2829.0067	5738.0135	0.0000	1.0000
F81G	39	-2830.3370	5738.6741	0.0000	1.0000
F81I	39	-2837.1254	5752.2508	0.0000	1.0000
SYM	40	-2838.7779	5757.5559	0.0000	1.0000
K2P	36	-2847.6069	5767.2138	0.0000	1.0000
JC69IG	37	-2847.1189	5768.2377	0.0000	1.0000
JC69G	36	-2848.4739	5768.9479	0.0000	1.0000
JC69I	36	-2855.1965	5782.3930	0.0000	1.0000
F81	38	-2891.2177	5858.4353	0.0000	1.0000
JC69	35	-2910.8314	5891.6628	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-2740.9572	5772.0083	0.9082	0.9082
GTRIG	45	-2740.0006	5776.6883	0.0875	0.9956
HKYG	40	-2759.6440	5783.0097	0.0037	0.9993
HKYIG	41	-2758.4731	5787.2609	0.0004	0.9998
GTRI	44	-2749.3252	5788.7443	0.0002	1.0000
HKYI	40	-2766.9829	5797.6875	0.0000	1.0000
K2PG	37	-2783.0939	5810.1305	0.0000	1.0000
K2PIG	38	-2781.7856	5814.1070	0.0000	1.0000
SYMG	41	-2774.7697	5819.8542	0.0000	1.0000
SYMIG	42	-2773.4071	5823.7221	0.0000	1.0000
K2PI	37	-2790.2368	5824.4162	0.0000	1.0000
SYMI	41	-2781.6660	5833.6468	0.0000	1.0000
GTR	43	-2803.8120	5891.1249	0.0000	1.0000
HKY	39	-2821.4339	5899.9966	0.0000	1.0000
F81G	39	-2830.3370	5917.8028	0.0000	1.0000
F81IG	40	-2829.0067	5921.7352	0.0000	1.0000
F81I	39	-2837.1254	5931.3795	0.0000	1.0000
K2P	36	-2847.6069	5932.5634	0.0000	1.0000
JC69G	36	-2848.4739	5934.2975	0.0000	1.0000
JC69IG	37	-2847.1189	5938.1804	0.0000	1.0000
SYM	40	-2838.7779	5941.2776	0.0000	1.0000
JC69I	36	-2855.1965	5947.7426	0.0000	1.0000
F81	38	-2891.2177	6032.9710	0.0000	1.0000
JC69	35	-2910.8314	6052.4193	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_8822.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8822.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/chr6_8822.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8822.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8822.phylip = 1 - 730;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8822.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;


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End of Output

