
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:07 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_360.phylip" (19 taxa, 826 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-3056.6441	6199.6811	0.4817	0.4817
HKYG	40	-3057.7555	6199.6892	0.4797	0.9614
GTRIG	45	-3055.3502	6206.0080	0.0204	0.9818
GTRG	44	-3056.5948	6206.2601	0.0180	0.9997
HKYI	40	-3065.3576	6214.8936	0.0002	1.0000
GTRI	44	-3064.1148	6221.3001	0.0000	1.0000
K2PIG	38	-3071.3532	6222.4725	0.0000	1.0000
K2PG	37	-3072.6503	6222.8690	0.0000	1.0000
SYMIG	42	-3069.3854	6227.3837	0.0000	1.0000
SYMG	41	-3070.5159	6227.4247	0.0000	1.0000
K2PI	37	-3079.7368	6237.0422	0.0000	1.0000
SYMI	41	-3077.8302	6242.0533	0.0000	1.0000
F81IG	40	-3125.5334	6335.2451	0.0000	1.0000
F81G	39	-3126.8903	6335.7500	0.0000	1.0000
F81I	39	-3132.7498	6347.4690	0.0000	1.0000
HKY	39	-3133.7707	6349.5109	0.0000	1.0000
JC69IG	37	-3137.2346	6352.0376	0.0000	1.0000
JC69G	36	-3138.4646	6352.3057	0.0000	1.0000
GTR	43	-3133.2347	6357.3082	0.0000	1.0000
JC69I	36	-3144.6277	6364.6318	0.0000	1.0000
K2P	36	-3148.1703	6371.7171	0.0000	1.0000
SYM	40	-3146.2085	6376.5952	0.0000	1.0000
F81	38	-3200.1267	6480.0195	0.0000	1.0000
JC69	35	-3211.6435	6496.4768	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-3056.6441	6195.2883	0.4965	0.4965
HKYG	40	-3057.7555	6195.5109	0.4442	0.9406
GTRIG	45	-3055.3502	6200.7003	0.0332	0.9738
GTRG	44	-3056.5948	6201.1896	0.0260	0.9998
HKYI	40	-3065.3576	6210.7152	0.0002	1.0000
GTRI	44	-3064.1148	6216.2297	0.0000	1.0000
K2PIG	38	-3071.3532	6218.7063	0.0000	1.0000
K2PG	37	-3072.6503	6219.3005	0.0000	1.0000
SYMIG	42	-3069.3854	6222.7707	0.0000	1.0000
SYMG	41	-3070.5159	6223.0318	0.0000	1.0000
K2PI	37	-3079.7368	6233.4737	0.0000	1.0000
SYMI	41	-3077.8302	6237.6605	0.0000	1.0000
F81IG	40	-3125.5334	6331.0668	0.0000	1.0000
F81G	39	-3126.8903	6331.7805	0.0000	1.0000
F81I	39	-3132.7498	6343.4995	0.0000	1.0000
HKY	39	-3133.7707	6345.5415	0.0000	1.0000
JC69IG	37	-3137.2346	6348.4691	0.0000	1.0000
JC69G	36	-3138.4646	6348.9292	0.0000	1.0000
GTR	43	-3133.2347	6352.4693	0.0000	1.0000
JC69I	36	-3144.6277	6361.2553	0.0000	1.0000
K2P	36	-3148.1703	6368.3406	0.0000	1.0000
SYM	40	-3146.2085	6372.4169	0.0000	1.0000
F81	38	-3200.1267	6476.2533	0.0000	1.0000
JC69	35	-3211.6435	6493.2869	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3057.7555	6384.1747	0.8966	0.8966
HKYIG	41	-3056.6441	6388.6687	0.0948	0.9914
K2PG	37	-3072.6503	6393.8145	0.0072	0.9986
K2PIG	38	-3071.3532	6397.9369	0.0009	0.9995
HKYI	40	-3065.3576	6399.3790	0.0004	1.0000
K2PI	37	-3079.7368	6407.9877	0.0000	1.0000
GTRG	44	-3056.5948	6408.7198	0.0000	1.0000
GTRIG	45	-3055.3502	6412.9471	0.0000	1.0000
SYMG	41	-3070.5159	6416.4122	0.0000	1.0000
SYMIG	42	-3069.3854	6420.8677	0.0000	1.0000
GTRI	44	-3064.1148	6423.7599	0.0000	1.0000
SYMI	41	-3077.8302	6431.0408	0.0000	1.0000
F81G	39	-3126.8903	6515.7277	0.0000	1.0000
JC69G	36	-3138.4646	6518.7267	0.0000	1.0000
F81IG	40	-3125.5334	6519.7306	0.0000	1.0000
JC69IG	37	-3137.2346	6522.9831	0.0000	1.0000
F81I	39	-3132.7498	6527.4467	0.0000	1.0000
HKY	39	-3133.7707	6529.4887	0.0000	1.0000
JC69I	36	-3144.6277	6531.0528	0.0000	1.0000
K2P	36	-3148.1703	6538.1381	0.0000	1.0000
GTR	43	-3133.2347	6555.2829	0.0000	1.0000
SYM	40	-3146.2085	6561.0807	0.0000	1.0000
F81	38	-3200.1267	6655.4839	0.0000	1.0000
JC69	35	-3211.6435	6658.3677	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_360.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_360.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_360.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_360.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) 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_360.phylip = 1 - 826;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_360.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

