
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:20 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_8812.phylip" (19 taxa, 713 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	-3916.7460	7929.6989	0.5834	0.5834
GTRG	44	-3918.2222	7930.3725	0.4166	1.0000
HKYIG	41	-3931.7526	7950.6378	0.0000	1.0000
HKYG	40	-3933.3477	7951.5764	0.0000	1.0000
GTRI	44	-3936.8462	7967.6206	0.0000	1.0000
SYMIG	42	-3939.9558	7969.3027	0.0000	1.0000
SYMG	41	-3941.6006	7970.3339	0.0000	1.0000
K2PIG	38	-3946.9700	7974.3377	0.0000	1.0000
K2PG	37	-3948.3757	7974.9172	0.0000	1.0000
HKYI	40	-3949.1263	7983.1336	0.0000	1.0000
SYMI	41	-3957.0119	8001.1564	0.0000	1.0000
K2PI	37	-3964.5231	8007.2121	0.0000	1.0000
GTR	43	-4067.2662	8226.1887	0.0000	1.0000
F81IG	40	-4071.3516	8227.5841	0.0000	1.0000
F81G	39	-4072.7092	8228.0543	0.0000	1.0000
HKY	39	-4077.5807	8237.7974	0.0000	1.0000
F81I	39	-4081.9005	8246.4369	0.0000	1.0000
SYM	40	-4081.8345	8248.5500	0.0000	1.0000
JC69IG	37	-4089.7883	8257.7425	0.0000	1.0000
K2P	36	-4091.4505	8258.8418	0.0000	1.0000
JC69G	36	-4091.4685	8258.8778	0.0000	1.0000
JC69I	36	-4101.8262	8279.5933	0.0000	1.0000
F81	38	-4204.5092	8489.4161	0.0000	1.0000
JC69	35	-4224.1637	8522.0497	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3916.7460	7923.4920	0.6168	0.6168
GTRG	44	-3918.2222	7924.4444	0.3831	1.0000
HKYIG	41	-3931.7526	7945.5051	0.0000	1.0000
HKYG	40	-3933.3477	7946.6955	0.0000	1.0000
GTRI	44	-3936.8462	7961.6924	0.0000	1.0000
SYMIG	42	-3939.9558	7963.9116	0.0000	1.0000
SYMG	41	-3941.6006	7965.2013	0.0000	1.0000
K2PIG	38	-3946.9700	7969.9401	0.0000	1.0000
K2PG	37	-3948.3757	7970.7513	0.0000	1.0000
HKYI	40	-3949.1263	7978.2526	0.0000	1.0000
SYMI	41	-3957.0119	7996.0238	0.0000	1.0000
K2PI	37	-3964.5231	8003.0461	0.0000	1.0000
GTR	43	-4067.2662	8220.5325	0.0000	1.0000
F81IG	40	-4071.3516	8222.7031	0.0000	1.0000
F81G	39	-4072.7092	8223.4183	0.0000	1.0000
HKY	39	-4077.5807	8233.1614	0.0000	1.0000
F81I	39	-4081.9005	8241.8010	0.0000	1.0000
SYM	40	-4081.8345	8243.6690	0.0000	1.0000
JC69IG	37	-4089.7883	8253.5766	0.0000	1.0000
K2P	36	-4091.4505	8254.9010	0.0000	1.0000
JC69G	36	-4091.4685	8254.9370	0.0000	1.0000
JC69I	36	-4101.8262	8275.6525	0.0000	1.0000
F81	38	-4204.5092	8485.0184	0.0000	1.0000
JC69	35	-4224.1637	8518.3274	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3918.2222	8125.5016	0.7534	0.7534
GTRIG	45	-3916.7460	8129.1186	0.1235	0.8769
HKYG	40	-3933.3477	8129.4747	0.1033	0.9802
HKYIG	41	-3931.7526	8132.8539	0.0191	0.9993
K2PG	37	-3948.3757	8139.8221	0.0006	0.9999
K2PIG	38	-3946.9700	8143.5804	0.0001	1.0000
SYMG	41	-3941.6006	8152.5500	0.0000	1.0000
SYMIG	42	-3939.9558	8155.8299	0.0000	1.0000
HKYI	40	-3949.1263	8161.0319	0.0000	1.0000
GTRI	44	-3936.8462	8162.7496	0.0000	1.0000
K2PI	37	-3964.5231	8172.1170	0.0000	1.0000
SYMI	41	-3957.0119	8183.3725	0.0000	1.0000
F81G	39	-4072.7092	8401.6281	0.0000	1.0000
F81IG	40	-4071.3516	8405.4824	0.0000	1.0000
HKY	39	-4077.5807	8411.3712	0.0000	1.0000
GTR	43	-4067.2662	8417.0202	0.0000	1.0000
K2P	36	-4091.4505	8419.4023	0.0000	1.0000
JC69G	36	-4091.4685	8419.4383	0.0000	1.0000
F81I	39	-4081.9005	8420.0108	0.0000	1.0000
JC69IG	37	-4089.7883	8422.6474	0.0000	1.0000
SYM	40	-4081.8345	8426.4483	0.0000	1.0000
JC69I	36	-4101.8262	8440.1538	0.0000	1.0000
F81	38	-4204.5092	8658.6587	0.0000	1.0000
JC69	35	-4224.1637	8678.2592	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/chr8_8812.phylip = 1 - 713;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8812.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/chr8_8812.phylip = 1 - 713;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8812.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/chr8_8812.phylip = 1 - 713;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_8812.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

