
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:17 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/chrZ_11420.phylip" (19 taxa, 600 characters)

Minimum AIC  model: GTRG
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	-1468.4347	3022.7370	0.3044	0.3044
GTRG	44	-1464.0529	3023.2410	0.2366	0.5409
HKYI	40	-1469.0779	3024.0234	0.1600	0.7009
GTRI	44	-1464.7422	3024.6195	0.1187	0.8196
HKYIG	41	-1468.4104	3024.9929	0.0985	0.9182
GTRIG	45	-1464.0376	3025.5481	0.0746	0.9928
HKY	39	-1473.9021	3031.3757	0.0041	0.9969
GTR	43	-1469.5386	3031.8830	0.0031	1.0000
K2PG	37	-1486.2522	3051.5079	0.0000	1.0000
K2PI	37	-1486.8759	3052.7554	0.0000	1.0000
K2PIG	38	-1486.2257	3053.7348	0.0000	1.0000
SYMG	41	-1483.8425	3055.8570	0.0000	1.0000
SYMI	41	-1484.4865	3057.1451	0.0000	1.0000
SYMIG	42	-1483.8226	3058.1300	0.0000	1.0000
K2P	36	-1491.8674	3060.4666	0.0000	1.0000
SYM	40	-1489.3070	3064.4816	0.0000	1.0000
F81G	39	-1494.2859	3072.1432	0.0000	1.0000
F81I	39	-1494.9976	3073.5667	0.0000	1.0000
F81IG	40	-1494.2894	3074.4465	0.0000	1.0000
F81	38	-1498.8026	3078.8885	0.0000	1.0000
JC69G	36	-1509.8507	3096.4331	0.0000	1.0000
JC69I	36	-1510.5594	3097.8505	0.0000	1.0000
JC69IG	37	-1509.8513	3098.7062	0.0000	1.0000
JC69	35	-1514.4748	3103.4177	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1464.0529	3016.1058	0.3131	0.3131
HKYG	40	-1468.4347	3016.8694	0.2138	0.5269
GTRI	44	-1464.7422	3017.4844	0.1572	0.6841
GTRIG	45	-1464.0376	3018.0752	0.1170	0.8011
HKYI	40	-1469.0779	3018.1558	0.1124	0.9134
HKYIG	41	-1468.4104	3018.8209	0.0806	0.9940
GTR	43	-1469.5386	3025.0772	0.0035	0.9975
HKY	39	-1473.9021	3025.8043	0.0025	1.0000
K2PG	37	-1486.2522	3046.5043	0.0000	1.0000
K2PI	37	-1486.8759	3047.7519	0.0000	1.0000
K2PIG	38	-1486.2257	3048.4514	0.0000	1.0000
SYMG	41	-1483.8425	3049.6850	0.0000	1.0000
SYMI	41	-1484.4865	3050.9730	0.0000	1.0000
SYMIG	42	-1483.8226	3051.6452	0.0000	1.0000
K2P	36	-1491.8674	3055.7348	0.0000	1.0000
SYM	40	-1489.3070	3058.6140	0.0000	1.0000
F81G	39	-1494.2859	3066.5718	0.0000	1.0000
F81I	39	-1494.9976	3067.9952	0.0000	1.0000
F81IG	40	-1494.2894	3068.5788	0.0000	1.0000
F81	38	-1498.8026	3073.6051	0.0000	1.0000
JC69G	36	-1509.8507	3091.7013	0.0000	1.0000
JC69I	36	-1510.5594	3093.1187	0.0000	1.0000
JC69IG	37	-1509.8513	3093.7026	0.0000	1.0000
JC69	35	-1514.4748	3098.9496	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1468.4347	3192.7466	0.5982	0.5982
HKYI	40	-1469.0779	3194.0330	0.3144	0.9126
HKY	39	-1473.9021	3197.2845	0.0619	0.9745
HKYIG	41	-1468.4104	3199.0950	0.0250	0.9995
K2PG	37	-1486.2522	3209.1907	0.0002	0.9997
GTRG	44	-1464.0529	3209.5707	0.0001	0.9998
K2PI	37	-1486.8759	3210.4383	0.0001	0.9999
GTRI	44	-1464.7422	3210.9493	0.0001	1.0000
K2P	36	-1491.8674	3214.0243	0.0000	1.0000
GTR	43	-1469.5386	3214.1452	0.0000	1.0000
K2PIG	38	-1486.2257	3215.5347	0.0000	1.0000
GTRIG	45	-1464.0376	3215.9371	0.0000	1.0000
SYMG	41	-1483.8425	3229.9591	0.0000	1.0000
SYMI	41	-1484.4865	3231.2472	0.0000	1.0000
SYM	40	-1489.3070	3234.4912	0.0000	1.0000
SYMIG	42	-1483.8226	3236.3163	0.0000	1.0000
F81G	39	-1494.2859	3238.0520	0.0000	1.0000
F81I	39	-1494.9976	3239.4755	0.0000	1.0000
F81	38	-1498.8026	3240.6884	0.0000	1.0000
F81IG	40	-1494.2894	3244.4560	0.0000	1.0000
JC69G	36	-1509.8507	3249.9908	0.0000	1.0000
JC69I	36	-1510.5594	3251.4082	0.0000	1.0000
JC69	35	-1514.4748	3252.8421	0.0000	1.0000
JC69IG	37	-1509.8513	3256.3890	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/chrZ_11420.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11420.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11420.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11420.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/chrZ_11420.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11420.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

