
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:40 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/chr11_3418.phylip" (19 taxa, 717 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3204.5568	6503.0064	0.4226	0.4226
HKYG	40	-3209.3645	6503.5810	0.3171	0.7397
GTRIG	45	-3204.4987	6505.1673	0.1435	0.8832
HKYIG	41	-3209.2392	6505.5805	0.1167	0.9999
HKYI	40	-3217.2740	6519.4000	0.0001	1.0000
GTRI	44	-3214.2829	6522.4587	0.0000	1.0000
K2PG	37	-3242.4379	6563.0172	0.0000	1.0000
K2PIG	38	-3242.2675	6564.9066	0.0000	1.0000
SYMG	41	-3241.8013	6570.7047	0.0000	1.0000
SYMIG	42	-3241.6298	6572.6186	0.0000	1.0000
K2PI	37	-3249.7624	6577.6662	0.0000	1.0000
SYMI	41	-3249.2590	6585.6202	0.0000	1.0000
HKY	39	-3281.2683	6645.1451	0.0000	1.0000
GTR	43	-3278.3979	6648.4184	0.0000	1.0000
F81G	39	-3298.4984	6679.6054	0.0000	1.0000
F81IG	40	-3298.4232	6681.6985	0.0000	1.0000
F81I	39	-3303.8565	6690.3215	0.0000	1.0000
K2P	36	-3312.7927	6701.5030	0.0000	1.0000
SYM	40	-3312.1836	6709.2193	0.0000	1.0000
JC69G	36	-3321.3900	6718.6976	0.0000	1.0000
JC69IG	37	-3321.3503	6720.8420	0.0000	1.0000
JC69I	36	-3326.4076	6728.7329	0.0000	1.0000
F81	38	-3363.2929	6806.9575	0.0000	1.0000
JC69	35	-3385.8345	6845.3695	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3204.5568	6497.1136	0.4946	0.4946
HKYG	40	-3209.3645	6498.7289	0.2205	0.7151
GTRIG	45	-3204.4987	6498.9974	0.1928	0.9079
HKYIG	41	-3209.2392	6500.4783	0.0920	0.9999
HKYI	40	-3217.2740	6514.5479	0.0001	1.0000
GTRI	44	-3214.2829	6516.5658	0.0000	1.0000
K2PG	37	-3242.4379	6558.8758	0.0000	1.0000
K2PIG	38	-3242.2675	6560.5350	0.0000	1.0000
SYMG	41	-3241.8013	6565.6025	0.0000	1.0000
SYMIG	42	-3241.6298	6567.2595	0.0000	1.0000
K2PI	37	-3249.7624	6573.5248	0.0000	1.0000
SYMI	41	-3249.2590	6580.5180	0.0000	1.0000
HKY	39	-3281.2683	6640.5365	0.0000	1.0000
GTR	43	-3278.3979	6642.7959	0.0000	1.0000
F81G	39	-3298.4984	6674.9968	0.0000	1.0000
F81IG	40	-3298.4232	6676.8464	0.0000	1.0000
F81I	39	-3303.8565	6685.7130	0.0000	1.0000
K2P	36	-3312.7927	6697.5854	0.0000	1.0000
SYM	40	-3312.1836	6704.3672	0.0000	1.0000
JC69G	36	-3321.3900	6714.7800	0.0000	1.0000
JC69IG	37	-3321.3503	6716.7006	0.0000	1.0000
JC69I	36	-3326.4076	6724.8152	0.0000	1.0000
F81	38	-3363.2929	6802.5858	0.0000	1.0000
JC69	35	-3385.8345	6841.6691	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3209.3645	6681.7319	0.9588	0.9588
HKYIG	41	-3209.2392	6688.0564	0.0406	0.9994
HKYI	40	-3217.2740	6697.5510	0.0004	0.9998
GTRG	44	-3204.5568	6698.4169	0.0002	1.0000
GTRIG	45	-3204.4987	6704.8758	0.0000	1.0000
GTRI	44	-3214.2829	6717.8691	0.0000	1.0000
K2PG	37	-3242.4379	6728.1536	0.0000	1.0000
K2PIG	38	-3242.2675	6734.3878	0.0000	1.0000
K2PI	37	-3249.7624	6742.8026	0.0000	1.0000
SYMG	41	-3241.8013	6753.1806	0.0000	1.0000
SYMIG	42	-3241.6298	6759.4127	0.0000	1.0000
SYMI	41	-3249.2590	6768.0961	0.0000	1.0000
HKY	39	-3281.2683	6818.9645	0.0000	1.0000
GTR	43	-3278.3979	6839.5241	0.0000	1.0000
F81G	39	-3298.4984	6853.4248	0.0000	1.0000
F81IG	40	-3298.4232	6859.8494	0.0000	1.0000
K2P	36	-3312.7927	6862.2881	0.0000	1.0000
F81I	39	-3303.8565	6864.1409	0.0000	1.0000
JC69G	36	-3321.3900	6879.4827	0.0000	1.0000
JC69IG	37	-3321.3503	6885.9784	0.0000	1.0000
SYM	40	-3312.1836	6887.3702	0.0000	1.0000
JC69I	36	-3326.4076	6889.5180	0.0000	1.0000
F81	38	-3363.2929	6976.4387	0.0000	1.0000
JC69	35	-3385.8345	7001.7967	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/chr11_3418.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3418.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3418.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3418.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3418.phylip = 1 - 717;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3418.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

