
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:18 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/chr3_6129.phylip" (19 taxa, 996 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-3012.0979	6118.5537	0.9252	0.9252
GTRG	44	-3015.7801	6123.7243	0.0697	0.9949
GTRI	44	-3018.4150	6128.9940	0.0050	0.9999
HKYIG	41	-3026.5802	6138.7704	0.0000	1.0000
HKYG	40	-3028.2932	6140.0210	0.0000	1.0000
SYMIG	42	-3029.6794	6147.1490	0.0000	1.0000
HKYI	40	-3033.5643	6150.5632	0.0000	1.0000
SYMG	41	-3033.8310	6153.2721	0.0000	1.0000
SYMI	41	-3036.6779	6158.9658	0.0000	1.0000
K2PIG	38	-3040.1712	6159.4396	0.0000	1.0000
K2PG	37	-3041.9522	6160.8396	0.0000	1.0000
K2PI	37	-3047.6337	6172.2026	0.0000	1.0000
GTR	43	-3075.4322	6240.8392	0.0000	1.0000
HKY	39	-3089.0089	6259.2815	0.0000	1.0000
SYM	40	-3091.1508	6265.7361	0.0000	1.0000
F81IG	40	-3097.3301	6278.0947	0.0000	1.0000
K2P	36	-3101.8146	6278.4071	0.0000	1.0000
F81G	39	-3101.9894	6285.2423	0.0000	1.0000
F81I	39	-3104.4938	6290.2513	0.0000	1.0000
JC69IG	37	-3107.6636	6292.2626	0.0000	1.0000
JC69G	36	-3112.6522	6300.0824	0.0000	1.0000
JC69I	36	-3115.3125	6305.4029	0.0000	1.0000
F81	38	-3155.3023	6389.7019	0.0000	1.0000
JC69	35	-3165.7224	6404.0698	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3012.0979	6114.1958	0.9317	0.9317
GTRG	44	-3015.7801	6119.5603	0.0637	0.9954
GTRI	44	-3018.4150	6124.8300	0.0046	1.0000
HKYIG	41	-3026.5802	6135.1603	0.0000	1.0000
HKYG	40	-3028.2932	6136.5865	0.0000	1.0000
SYMIG	42	-3029.6794	6143.3589	0.0000	1.0000
HKYI	40	-3033.5643	6147.1286	0.0000	1.0000
SYMG	41	-3033.8310	6149.6620	0.0000	1.0000
SYMI	41	-3036.6779	6155.3558	0.0000	1.0000
K2PIG	38	-3040.1712	6156.3424	0.0000	1.0000
K2PG	37	-3041.9522	6157.9044	0.0000	1.0000
K2PI	37	-3047.6337	6169.2673	0.0000	1.0000
GTR	43	-3075.4322	6236.8644	0.0000	1.0000
HKY	39	-3089.0089	6256.0179	0.0000	1.0000
SYM	40	-3091.1508	6262.3016	0.0000	1.0000
F81IG	40	-3097.3301	6274.6601	0.0000	1.0000
K2P	36	-3101.8146	6275.6292	0.0000	1.0000
F81G	39	-3101.9894	6281.9787	0.0000	1.0000
F81I	39	-3104.4938	6286.9877	0.0000	1.0000
JC69IG	37	-3107.6636	6289.3273	0.0000	1.0000
JC69G	36	-3112.6522	6297.3045	0.0000	1.0000
JC69I	36	-3115.3125	6302.6250	0.0000	1.0000
F81	38	-3155.3023	6386.6047	0.0000	1.0000
JC69	35	-3165.7224	6401.4448	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3028.2932	6332.7364	0.5365	0.5365
GTRIG	45	-3012.0979	6334.8644	0.1851	0.7217
GTRG	44	-3015.7801	6335.3251	0.1470	0.8687
HKYIG	41	-3026.5802	6336.2140	0.0943	0.9630
K2PG	37	-3041.9522	6339.3430	0.0197	0.9827
GTRI	44	-3018.4150	6340.5949	0.0105	0.9933
K2PIG	38	-3040.1712	6342.6848	0.0037	0.9970
HKYI	40	-3033.5643	6343.2785	0.0028	0.9997
SYMIG	42	-3029.6794	6349.3163	0.0001	0.9999
K2PI	37	-3047.6337	6350.7059	0.0001	0.9999
SYMG	41	-3033.8310	6350.7157	0.0001	1.0000
SYMI	41	-3036.6779	6356.4094	0.0000	1.0000
HKY	39	-3089.0089	6447.2640	0.0000	1.0000
GTR	43	-3075.4322	6447.7256	0.0000	1.0000
K2P	36	-3101.8146	6452.1641	0.0000	1.0000
SYM	40	-3091.1508	6458.4515	0.0000	1.0000
JC69IG	37	-3107.6636	6470.7659	0.0000	1.0000
F81IG	40	-3097.3301	6470.8100	0.0000	1.0000
F81G	39	-3101.9894	6473.2249	0.0000	1.0000
JC69G	36	-3112.6522	6473.8394	0.0000	1.0000
F81I	39	-3104.4938	6478.2338	0.0000	1.0000
JC69I	36	-3115.3125	6479.1599	0.0000	1.0000
F81	38	-3155.3023	6572.9471	0.0000	1.0000
JC69	35	-3165.7224	6573.0759	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6129.phylip = 1 - 996;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6129.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6129.phylip = 1 - 996;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6129.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr3_6129.phylip = 1 - 996;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6129.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

