
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:16 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/chr8_4221.phylip" (19 taxa, 535 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	-1470.4940	3027.6278	0.5478	0.5478
HKYIG	41	-1470.2894	3029.5646	0.2080	0.7558
HKYI	40	-1471.5679	3029.7754	0.1872	0.9430
GTRG	44	-1468.5677	3033.2171	0.0335	0.9765
GTRIG	45	-1468.3593	3035.1849	0.0125	0.9890
GTRI	44	-1469.6850	3035.4517	0.0110	1.0000
HKY	39	-1488.8938	3062.0907	0.0000	1.0000
GTR	43	-1486.6985	3067.1038	0.0000	1.0000
K2PG	37	-1501.2773	3082.2126	0.0000	1.0000
K2PI	37	-1501.9022	3083.4623	0.0000	1.0000
K2PIG	38	-1501.1930	3084.3617	0.0000	1.0000
SYMG	41	-1501.1098	3091.2054	0.0000	1.0000
F81G	39	-1503.7877	3091.8784	0.0000	1.0000
SYMI	41	-1501.7068	3092.3995	0.0000	1.0000
F81I	39	-1504.4229	3093.1489	0.0000	1.0000
SYMIG	42	-1501.0313	3093.4041	0.0000	1.0000
F81IG	40	-1503.7288	3094.0973	0.0000	1.0000
K2P	36	-1518.9167	3115.1829	0.0000	1.0000
F81	38	-1520.7745	3123.5247	0.0000	1.0000
SYM	40	-1518.6579	3123.9555	0.0000	1.0000
JC69G	36	-1530.3706	3138.0907	0.0000	1.0000
JC69I	36	-1530.8929	3139.1353	0.0000	1.0000
JC69IG	37	-1530.3366	3140.3311	0.0000	1.0000
JC69	35	-1547.4789	3170.0079	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1470.4940	3020.9881	0.4958	0.4958
HKYIG	41	-1470.2894	3022.5788	0.2238	0.7196
HKYI	40	-1471.5679	3023.1358	0.1694	0.8890
GTRG	44	-1468.5677	3025.1355	0.0623	0.9514
GTRIG	45	-1468.3593	3026.7186	0.0282	0.9796
GTRI	44	-1469.6850	3027.3700	0.0204	1.0000
HKY	39	-1488.8938	3055.7877	0.0000	1.0000
GTR	43	-1486.6985	3059.3970	0.0000	1.0000
K2PG	37	-1501.2773	3076.5547	0.0000	1.0000
K2PI	37	-1501.9022	3077.8044	0.0000	1.0000
K2PIG	38	-1501.1930	3078.3859	0.0000	1.0000
SYMG	41	-1501.1098	3084.2196	0.0000	1.0000
SYMI	41	-1501.7068	3085.4137	0.0000	1.0000
F81G	39	-1503.7877	3085.5753	0.0000	1.0000
SYMIG	42	-1501.0313	3086.0627	0.0000	1.0000
F81I	39	-1504.4229	3086.8459	0.0000	1.0000
F81IG	40	-1503.7288	3087.4577	0.0000	1.0000
K2P	36	-1518.9167	3109.8335	0.0000	1.0000
SYM	40	-1518.6579	3117.3159	0.0000	1.0000
F81	38	-1520.7745	3117.5489	0.0000	1.0000
JC69G	36	-1530.3706	3132.7413	0.0000	1.0000
JC69I	36	-1530.8929	3133.7859	0.0000	1.0000
JC69IG	37	-1530.3366	3134.6732	0.0000	1.0000
JC69	35	-1547.4789	3164.9578	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1470.4940	3192.2787	0.7170	0.7170
HKYI	40	-1471.5679	3194.4264	0.2450	0.9619
HKYIG	41	-1470.2894	3198.1517	0.0380	1.0000
GTRG	44	-1468.5677	3213.5552	0.0000	1.0000
GTRI	44	-1469.6850	3215.7898	0.0000	1.0000
GTRIG	45	-1468.3593	3219.4206	0.0000	1.0000
HKY	39	-1488.8938	3222.7961	0.0000	1.0000
K2PG	37	-1501.2773	3234.9985	0.0000	1.0000
K2PI	37	-1501.9022	3236.2483	0.0000	1.0000
K2PIG	38	-1501.1930	3241.1120	0.0000	1.0000
GTR	43	-1486.6985	3243.5345	0.0000	1.0000
F81G	39	-1503.7877	3252.5837	0.0000	1.0000
F81I	39	-1504.4229	3253.8543	0.0000	1.0000
F81IG	40	-1503.7288	3258.7483	0.0000	1.0000
SYMG	41	-1501.1098	3259.7926	0.0000	1.0000
SYMI	41	-1501.7068	3260.9866	0.0000	1.0000
K2P	36	-1518.9167	3263.9951	0.0000	1.0000
SYMIG	42	-1501.0313	3265.9179	0.0000	1.0000
F81	38	-1520.7745	3280.2751	0.0000	1.0000
JC69G	36	-1530.3706	3286.9029	0.0000	1.0000
JC69I	36	-1530.8929	3287.9475	0.0000	1.0000
SYM	40	-1518.6579	3288.6065	0.0000	1.0000
JC69IG	37	-1530.3366	3293.1170	0.0000	1.0000
JC69	35	-1547.4789	3314.8372	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/chr8_4221.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4221.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/chr8_4221.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4221.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/chr8_4221.phylip = 1 - 535;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4221.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

