
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:32 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/chr6_3258.phylip" (19 taxa, 859 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	-2769.6467	5632.1584	0.5962	0.5962
GTRIG	45	-2768.9378	5632.9679	0.3977	0.9939
GTRI	44	-2774.4345	5641.7338	0.0050	0.9989
HKYG	40	-2780.5298	5645.0693	0.0009	0.9998
HKYIG	41	-2780.9894	5648.1942	0.0002	1.0000
HKYI	40	-2785.4088	5654.8273	0.0000	1.0000
SYMG	41	-2799.4570	5685.1294	0.0000	1.0000
SYMIG	42	-2799.8782	5688.1828	0.0000	1.0000
SYMI	41	-2804.0443	5694.3040	0.0000	1.0000
K2PG	37	-2809.1926	5695.8102	0.0000	1.0000
K2PIG	38	-2808.5316	5696.6779	0.0000	1.0000
K2PI	37	-2812.7834	5702.9918	0.0000	1.0000
GTR	43	-2812.9107	5716.4643	0.0000	1.0000
HKY	39	-2823.9579	5729.7254	0.0000	1.0000
F81G	39	-2832.5981	5747.0058	0.0000	1.0000
F81IG	40	-2832.1016	5748.2130	0.0000	1.0000
F81I	39	-2835.8134	5753.4363	0.0000	1.0000
SYM	40	-2843.1653	5770.3403	0.0000	1.0000
K2P	36	-2852.4361	5780.1130	0.0000	1.0000
JC69G	36	-2857.4996	5790.2401	0.0000	1.0000
JC69IG	37	-2857.0309	5791.4869	0.0000	1.0000
JC69I	36	-2860.5765	5796.3939	0.0000	1.0000
F81	38	-2874.7413	5829.0972	0.0000	1.0000
JC69	35	-2899.3199	5871.7018	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2769.6467	5627.2935	0.5691	0.5691
GTRIG	45	-2768.9378	5627.8757	0.4254	0.9945
GTRI	44	-2774.4345	5636.8690	0.0047	0.9993
HKYG	40	-2780.5298	5641.0595	0.0006	0.9999
HKYIG	41	-2780.9894	5643.9788	0.0001	1.0000
HKYI	40	-2785.4088	5650.8176	0.0000	1.0000
SYMG	41	-2799.4570	5680.9140	0.0000	1.0000
SYMIG	42	-2799.8782	5683.7563	0.0000	1.0000
SYMI	41	-2804.0443	5690.0886	0.0000	1.0000
K2PG	37	-2809.1926	5692.3851	0.0000	1.0000
K2PIG	38	-2808.5316	5693.0633	0.0000	1.0000
K2PI	37	-2812.7834	5699.5667	0.0000	1.0000
GTR	43	-2812.9107	5711.8214	0.0000	1.0000
HKY	39	-2823.9579	5725.9158	0.0000	1.0000
F81G	39	-2832.5981	5743.1962	0.0000	1.0000
F81IG	40	-2832.1016	5744.2032	0.0000	1.0000
F81I	39	-2835.8134	5749.6267	0.0000	1.0000
SYM	40	-2843.1653	5766.3306	0.0000	1.0000
K2P	36	-2852.4361	5776.8721	0.0000	1.0000
JC69G	36	-2857.4996	5786.9992	0.0000	1.0000
JC69IG	37	-2857.0309	5788.0618	0.0000	1.0000
JC69I	36	-2860.5765	5793.1530	0.0000	1.0000
F81	38	-2874.7413	5825.4826	0.0000	1.0000
JC69	35	-2899.3199	5868.6398	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2780.5298	5831.2903	0.9034	0.9034
GTRG	44	-2769.6467	5836.5473	0.0652	0.9686
HKYIG	41	-2780.9894	5838.9653	0.0195	0.9881
HKYI	40	-2785.4088	5841.0483	0.0069	0.9949
GTRIG	45	-2768.9378	5841.8853	0.0045	0.9995
GTRI	44	-2774.4345	5846.1228	0.0005	1.0000
K2PG	37	-2809.1926	5868.3486	0.0000	1.0000
K2PIG	38	-2808.5316	5873.7825	0.0000	1.0000
K2PI	37	-2812.7834	5875.5302	0.0000	1.0000
SYMG	41	-2799.4570	5875.9005	0.0000	1.0000
SYMIG	42	-2799.8782	5883.4986	0.0000	1.0000
SYMI	41	-2804.0443	5885.0751	0.0000	1.0000
HKY	39	-2823.9579	5911.3908	0.0000	1.0000
GTR	43	-2812.9107	5916.3194	0.0000	1.0000
F81G	39	-2832.5981	5928.6712	0.0000	1.0000
F81IG	40	-2832.1016	5934.4340	0.0000	1.0000
F81I	39	-2835.8134	5935.1017	0.0000	1.0000
K2P	36	-2852.4361	5948.0798	0.0000	1.0000
SYM	40	-2843.1653	5956.5613	0.0000	1.0000
JC69G	36	-2857.4996	5958.2069	0.0000	1.0000
JC69IG	37	-2857.0309	5964.0253	0.0000	1.0000
JC69I	36	-2860.5765	5964.3607	0.0000	1.0000
F81	38	-2874.7413	6006.2018	0.0000	1.0000
JC69	35	-2899.3199	6035.0917	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_3258.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3258.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_3258.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3258.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/chr6_3258.phylip = 1 - 859;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3258.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

