
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:32 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/chr1_15369.phylip" (19 taxa, 856 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: K2PG


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
SYMG	41	-4638.3514	9362.9338	0.5980	0.5980
SYMIG	42	-4638.3515	9365.1457	0.1979	0.7959
GTRG	44	-4636.6235	9366.1299	0.1210	0.9169
GTRIG	45	-4636.1325	9367.3762	0.0649	0.9817
HKYG	40	-4643.2909	9370.6063	0.0129	0.9946
HKYIG	41	-4643.2907	9372.8124	0.0043	0.9989
K2PG	37	-4649.3428	9376.1233	0.0008	0.9997
K2PIG	38	-4649.3428	9378.3135	0.0003	1.0000
SYMI	41	-4663.8632	9413.9574	0.0000	1.0000
GTRI	44	-4662.3964	9417.6756	0.0000	1.0000
HKYI	40	-4670.6741	9425.3727	0.0000	1.0000
K2PI	37	-4676.5189	9430.4755	0.0000	1.0000
SYM	40	-4724.5981	9533.2207	0.0000	1.0000
GTR	43	-4722.5724	9535.8048	0.0000	1.0000
HKY	39	-4734.4000	9550.6235	0.0000	1.0000
K2P	36	-4740.3285	9555.9097	0.0000	1.0000
F81G	39	-4755.5085	9592.8404	0.0000	1.0000
F81IG	40	-4755.5108	9595.0461	0.0000	1.0000
JC69G	36	-4762.7717	9600.7961	0.0000	1.0000
JC69IG	37	-4762.7715	9602.9806	0.0000	1.0000
F81I	39	-4778.6144	9639.0524	0.0000	1.0000
JC69I	36	-4784.7076	9644.6680	0.0000	1.0000
F81	38	-4841.4738	9762.5755	0.0000	1.0000
JC69	35	-4846.1728	9765.4187	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-4638.3514	9358.7029	0.5422	0.5422
SYMIG	42	-4638.3515	9360.7029	0.1994	0.7416
GTRG	44	-4636.6235	9361.2470	0.1519	0.8936
GTRIG	45	-4636.1325	9362.2651	0.0913	0.9849
HKYG	40	-4643.2909	9366.5818	0.0106	0.9954
HKYIG	41	-4643.2907	9368.5815	0.0039	0.9993
K2PG	37	-4649.3428	9372.6857	0.0005	0.9998
K2PIG	38	-4649.3428	9374.6856	0.0002	1.0000
SYMI	41	-4663.8632	9409.7264	0.0000	1.0000
GTRI	44	-4662.3964	9412.7927	0.0000	1.0000
HKYI	40	-4670.6741	9421.3481	0.0000	1.0000
K2PI	37	-4676.5189	9427.0379	0.0000	1.0000
SYM	40	-4724.5981	9529.1962	0.0000	1.0000
GTR	43	-4722.5724	9531.1447	0.0000	1.0000
HKY	39	-4734.4000	9546.8000	0.0000	1.0000
K2P	36	-4740.3285	9552.6570	0.0000	1.0000
F81G	39	-4755.5085	9589.0169	0.0000	1.0000
F81IG	40	-4755.5108	9591.0215	0.0000	1.0000
JC69G	36	-4762.7717	9597.5433	0.0000	1.0000
JC69IG	37	-4762.7715	9599.5429	0.0000	1.0000
F81I	39	-4778.6144	9635.2288	0.0000	1.0000
JC69I	36	-4784.7076	9641.4153	0.0000	1.0000
F81	38	-4841.4738	9758.9476	0.0000	1.0000
JC69	35	-4846.1728	9762.3455	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-4649.3428	9548.5197	0.8806	0.8806
SYMG	41	-4638.3514	9553.5460	0.0713	0.9520
K2PIG	38	-4649.3428	9555.2719	0.0301	0.9821
HKYG	40	-4643.2909	9556.6726	0.0149	0.9970
SYMIG	42	-4638.3515	9560.2983	0.0024	0.9995
HKYIG	41	-4643.2907	9563.4246	0.0005	1.0000
GTRG	44	-4636.6235	9570.3469	0.0000	1.0000
GTRIG	45	-4636.1325	9576.1172	0.0000	1.0000
K2PI	37	-4676.5189	9602.8719	0.0000	1.0000
SYMI	41	-4663.8632	9604.5695	0.0000	1.0000
HKYI	40	-4670.6741	9611.4390	0.0000	1.0000
GTRI	44	-4662.3964	9621.8926	0.0000	1.0000
SYM	40	-4724.5981	9719.2870	0.0000	1.0000
K2P	36	-4740.3285	9723.7387	0.0000	1.0000
HKY	39	-4734.4000	9732.1386	0.0000	1.0000
GTR	43	-4722.5724	9735.4923	0.0000	1.0000
JC69G	36	-4762.7717	9768.6251	0.0000	1.0000
F81G	39	-4755.5085	9774.3555	0.0000	1.0000
JC69IG	37	-4762.7715	9775.3769	0.0000	1.0000
F81IG	40	-4755.5108	9781.1124	0.0000	1.0000
JC69I	36	-4784.7076	9812.4970	0.0000	1.0000
F81I	39	-4778.6144	9820.5674	0.0000	1.0000
JC69	35	-4846.1728	9928.6750	0.0000	1.0000
F81	38	-4841.4738	9939.5339	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.phylip = 1 - 856;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.phylip = 1 - 856;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.phylip = 1 - 856;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15369.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

