
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:03 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/chr1_25693.phylip" (19 taxa, 525 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	-1392.0385	2873.2074	0.3788	0.3788
HKYG	40	-1393.4441	2873.6651	0.3013	0.6800
HKYI	40	-1393.8417	2874.4602	0.2024	0.8825
GTRIG	45	-1389.4113	2877.4656	0.0451	0.9275
GTRG	44	-1390.6369	2877.5238	0.0438	0.9713
GTRI	44	-1391.0790	2878.4080	0.0281	0.9994
K2PIG	38	-1402.7524	2887.6036	0.0003	0.9997
K2PG	37	-1404.3791	2888.5324	0.0002	0.9998
K2PI	37	-1404.6915	2889.1570	0.0001	1.0000
SYMIG	42	-1401.5142	2894.5221	0.0000	1.0000
SYMG	41	-1403.0129	2895.1562	0.0000	1.0000
SYMI	41	-1403.3173	2895.7651	0.0000	1.0000
F81G	39	-1415.3342	2915.1013	0.0000	1.0000
F81I	39	-1415.6221	2915.6771	0.0000	1.0000
F81IG	40	-1415.9817	2918.7403	0.0000	1.0000
HKY	39	-1421.1327	2926.6983	0.0000	1.0000
JC69G	36	-1426.0044	2929.4679	0.0000	1.0000
JC69IG	37	-1425.0689	2929.9120	0.0000	1.0000
GTR	43	-1418.0291	2929.9251	0.0000	1.0000
JC69I	36	-1426.2797	2930.0184	0.0000	1.0000
K2P	36	-1433.0367	2943.5323	0.0000	1.0000
SYM	40	-1431.4283	2949.6334	0.0000	1.0000
F81	38	-1441.2504	2964.5996	0.0000	1.0000
JC69	35	-1452.4309	2980.0152	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1392.0385	2866.0769	0.3702	0.3702
HKYG	40	-1393.4441	2866.8883	0.2468	0.6170
HKYI	40	-1393.8417	2867.6834	0.1658	0.7829
GTRIG	45	-1389.4113	2868.8226	0.0938	0.8767
GTRG	44	-1390.6369	2869.2738	0.0749	0.9515
GTRI	44	-1391.0790	2870.1580	0.0481	0.9997
K2PIG	38	-1402.7524	2881.5048	0.0002	0.9998
K2PG	37	-1404.3791	2882.7582	0.0001	0.9999
K2PI	37	-1404.6915	2883.3829	0.0001	1.0000
SYMIG	42	-1401.5142	2887.0283	0.0000	1.0000
SYMG	41	-1403.0129	2888.0257	0.0000	1.0000
SYMI	41	-1403.3173	2888.6347	0.0000	1.0000
F81G	39	-1415.3342	2908.6684	0.0000	1.0000
F81I	39	-1415.6221	2909.2441	0.0000	1.0000
F81IG	40	-1415.9817	2911.9634	0.0000	1.0000
HKY	39	-1421.1327	2920.2653	0.0000	1.0000
GTR	43	-1418.0291	2922.0582	0.0000	1.0000
JC69G	36	-1426.0044	2924.0089	0.0000	1.0000
JC69IG	37	-1425.0689	2924.1379	0.0000	1.0000
JC69I	36	-1426.2797	2924.5593	0.0000	1.0000
K2P	36	-1433.0367	2938.0733	0.0000	1.0000
SYM	40	-1431.4283	2942.8566	0.0000	1.0000
F81	38	-1441.2504	2958.5008	0.0000	1.0000
JC69	35	-1452.4309	2974.8618	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1393.4441	3037.4242	0.4407	0.4407
HKYI	40	-1393.8417	3038.2193	0.2962	0.7369
K2PG	37	-1404.3791	3040.5040	0.0945	0.8314
HKYIG	41	-1392.0385	3040.8763	0.0784	0.9098
K2PI	37	-1404.6915	3041.1287	0.0691	0.9790
K2PIG	38	-1402.7524	3043.5140	0.0210	0.9999
GTRG	44	-1390.6369	3056.8633	0.0000	1.0000
GTRI	44	-1391.0790	3057.7475	0.0000	1.0000
GTRIG	45	-1389.4113	3060.6755	0.0000	1.0000
SYMG	41	-1403.0129	3062.8251	0.0000	1.0000
SYMI	41	-1403.3173	3063.4340	0.0000	1.0000
SYMIG	42	-1401.5142	3066.0911	0.0000	1.0000
F81G	39	-1415.3342	3074.9409	0.0000	1.0000
F81I	39	-1415.6221	3075.5167	0.0000	1.0000
JC69G	36	-1426.0044	3077.4912	0.0000	1.0000
JC69I	36	-1426.2797	3078.0417	0.0000	1.0000
JC69IG	37	-1425.0689	3081.8836	0.0000	1.0000
F81IG	40	-1415.9817	3082.4994	0.0000	1.0000
HKY	39	-1421.1327	3086.5379	0.0000	1.0000
K2P	36	-1433.0367	3091.5556	0.0000	1.0000
GTR	43	-1418.0291	3105.3843	0.0000	1.0000
SYM	40	-1431.4283	3113.3925	0.0000	1.0000
F81	38	-1441.2504	3120.5099	0.0000	1.0000
JC69	35	-1452.4309	3124.0808	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/chr1_25693.phylip = 1 - 525;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25693.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/chr1_25693.phylip = 1 - 525;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25693.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/chr1_25693.phylip = 1 - 525;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25693.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

