
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:51 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/chr7_1380.phylip" (19 taxa, 779 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: GTRG


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	-3841.5703	7778.7886	0.8115	0.8115
GTRG	44	-3844.1564	7781.7080	0.1885	1.0000
SYMIG	42	-3855.4266	7799.7607	0.0000	1.0000
HKYIG	41	-3857.9631	7802.5992	0.0000	1.0000
SYMG	41	-3858.1751	7803.0232	0.0000	1.0000
HKYG	40	-3860.5789	7805.6023	0.0000	1.0000
GTRI	44	-3861.5913	7816.5777	0.0000	1.0000
K2PIG	38	-3879.6874	7839.3801	0.0000	1.0000
HKYI	40	-3878.0380	7840.5204	0.0000	1.0000
K2PG	37	-3882.3064	7842.4076	0.0000	1.0000
SYMI	41	-3877.9109	7842.4949	0.0000	1.0000
K2PI	37	-3898.9773	7875.7495	0.0000	1.0000
F81IG	40	-3911.9389	7908.3222	0.0000	1.0000
F81G	39	-3914.3590	7910.9400	0.0000	1.0000
F81I	39	-3927.5986	7937.4192	0.0000	1.0000
JC69IG	37	-3943.7867	7965.3682	0.0000	1.0000
JC69G	36	-3946.1026	7967.7956	0.0000	1.0000
JC69I	36	-3959.3823	7994.3550	0.0000	1.0000
GTR	43	-4010.8463	8112.8410	0.0000	1.0000
SYM	40	-4023.0034	8130.4512	0.0000	1.0000
HKY	39	-4026.8326	8135.8872	0.0000	1.0000
K2P	36	-4046.8263	8169.2428	0.0000	1.0000
F81	38	-4076.8682	8233.7419	0.0000	1.0000
JC69	35	-4104.0884	8281.5685	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3841.5703	7773.1406	0.8301	0.8301
GTRG	44	-3844.1564	7776.3129	0.1699	1.0000
SYMIG	42	-3855.4266	7794.8531	0.0000	1.0000
HKYIG	41	-3857.9631	7797.9262	0.0000	1.0000
SYMG	41	-3858.1751	7798.3502	0.0000	1.0000
HKYG	40	-3860.5789	7801.1579	0.0000	1.0000
GTRI	44	-3861.5913	7811.1826	0.0000	1.0000
K2PIG	38	-3879.6874	7835.3747	0.0000	1.0000
HKYI	40	-3878.0380	7836.0759	0.0000	1.0000
SYMI	41	-3877.9109	7837.8219	0.0000	1.0000
K2PG	37	-3882.3064	7838.6127	0.0000	1.0000
K2PI	37	-3898.9773	7871.9546	0.0000	1.0000
F81IG	40	-3911.9389	7903.8777	0.0000	1.0000
F81G	39	-3914.3590	7906.7181	0.0000	1.0000
F81I	39	-3927.5986	7933.1973	0.0000	1.0000
JC69IG	37	-3943.7867	7961.5733	0.0000	1.0000
JC69G	36	-3946.1026	7964.2053	0.0000	1.0000
JC69I	36	-3959.3823	7990.7647	0.0000	1.0000
GTR	43	-4010.8463	8107.6927	0.0000	1.0000
SYM	40	-4023.0034	8126.0068	0.0000	1.0000
HKY	39	-4026.8326	8131.6652	0.0000	1.0000
K2P	36	-4046.8263	8165.6525	0.0000	1.0000
F81	38	-4076.8682	8229.7365	0.0000	1.0000
JC69	35	-4104.0884	8278.1768	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3844.1564	7981.2653	0.6369	0.6369
GTRIG	45	-3841.5703	7982.7511	0.3030	0.9399
HKYG	40	-3860.5789	7987.4783	0.0285	0.9684
HKYIG	41	-3857.9631	7988.9046	0.0140	0.9824
SYMG	41	-3858.1751	7989.3286	0.0113	0.9937
SYMIG	42	-3855.4266	7990.4896	0.0063	1.0000
K2PG	37	-3882.3064	8010.9591	0.0000	1.0000
K2PIG	38	-3879.6874	8012.3791	0.0000	1.0000
GTRI	44	-3861.5913	8016.1351	0.0000	1.0000
HKYI	40	-3878.0380	8022.3964	0.0000	1.0000
SYMI	41	-3877.9109	8028.8003	0.0000	1.0000
K2PI	37	-3898.9773	8044.3010	0.0000	1.0000
F81G	39	-3914.3590	8088.3805	0.0000	1.0000
F81IG	40	-3911.9389	8090.1982	0.0000	1.0000
F81I	39	-3927.5986	8114.8597	0.0000	1.0000
JC69G	36	-3946.1026	8131.8937	0.0000	1.0000
JC69IG	37	-3943.7867	8133.9197	0.0000	1.0000
JC69I	36	-3959.3823	8158.4531	0.0000	1.0000
GTR	43	-4010.8463	8307.9872	0.0000	1.0000
SYM	40	-4023.0034	8312.3272	0.0000	1.0000
HKY	39	-4026.8326	8313.3277	0.0000	1.0000
K2P	36	-4046.8263	8333.3409	0.0000	1.0000
F81	38	-4076.8682	8406.7409	0.0000	1.0000
JC69	35	-4104.0884	8441.2072	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/chr7_1380.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1380.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/chr7_1380.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1380.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1380.phylip = 1 - 779;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1380.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;


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End of Output

