
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:59 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_3116.phylip" (19 taxa, 507 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	-1378.5320	2846.4705	0.5404	0.5404
HKYG	40	-1380.2661	2847.5708	0.3117	0.8521
HKYI	40	-1381.7271	2850.4927	0.0723	0.9244
GTRIG	45	-1376.2864	2851.5532	0.0426	0.9670
GTRG	44	-1378.0049	2852.5812	0.0255	0.9924
GTRI	44	-1379.5770	2855.7254	0.0053	0.9977
K2PIG	38	-1388.0629	2858.4591	0.0013	0.9990
K2PG	37	-1389.8659	2859.7275	0.0007	0.9998
K2PI	37	-1391.2811	2862.5580	0.0002	0.9999
SYMIG	42	-1386.8801	2865.5448	0.0000	1.0000
SYMG	41	-1388.7125	2866.8314	0.0000	1.0000
SYMI	41	-1390.1900	2869.7865	0.0000	1.0000
HKY	39	-1404.1307	2892.9424	0.0000	1.0000
GTR	43	-1401.5671	2897.3070	0.0000	1.0000
K2P	36	-1414.3102	2906.2884	0.0000	1.0000
SYM	40	-1412.7302	2912.4990	0.0000	1.0000
F81IG	40	-1416.9024	2920.8433	0.0000	1.0000
F81G	39	-1418.2878	2921.2566	0.0000	1.0000
F81I	39	-1419.7219	2924.1248	0.0000	1.0000
JC69IG	37	-1425.0893	2930.1744	0.0000	1.0000
JC69G	36	-1426.5372	2930.7424	0.0000	1.0000
JC69I	36	-1427.9338	2933.5356	0.0000	1.0000
F81	38	-1440.7378	2963.8090	0.0000	1.0000
JC69	35	-1449.6154	2974.5811	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1378.5320	2839.0641	0.5352	0.5352
HKYG	40	-1380.2661	2840.5322	0.2569	0.7920
GTRIG	45	-1376.2864	2842.5727	0.0926	0.8846
HKYI	40	-1381.7271	2843.4541	0.0596	0.9442
GTRG	44	-1378.0049	2844.0097	0.0451	0.9893
GTRI	44	-1379.5770	2847.1540	0.0094	0.9987
K2PIG	38	-1388.0629	2852.1257	0.0008	0.9995
K2PG	37	-1389.8659	2853.7318	0.0003	0.9998
K2PI	37	-1391.2811	2856.5622	0.0001	0.9999
SYMIG	42	-1386.8801	2857.7603	0.0000	1.0000
SYMG	41	-1388.7125	2859.4249	0.0000	1.0000
SYMI	41	-1390.1900	2862.3801	0.0000	1.0000
HKY	39	-1404.1307	2886.2615	0.0000	1.0000
GTR	43	-1401.5671	2889.1342	0.0000	1.0000
K2P	36	-1414.3102	2900.6203	0.0000	1.0000
SYM	40	-1412.7302	2905.4604	0.0000	1.0000
F81IG	40	-1416.9024	2913.8047	0.0000	1.0000
F81G	39	-1418.2878	2914.5757	0.0000	1.0000
F81I	39	-1419.7219	2917.4439	0.0000	1.0000
JC69IG	37	-1425.0893	2924.1787	0.0000	1.0000
JC69G	36	-1426.5372	2925.0743	0.0000	1.0000
JC69I	36	-1427.9338	2927.8675	0.0000	1.0000
F81	38	-1440.7378	2957.4757	0.0000	1.0000
JC69	35	-1449.6154	2969.2307	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1380.2661	3009.6727	0.3769	0.3769
K2PG	37	-1389.8659	3010.1867	0.2915	0.6684
HKYIG	41	-1378.5320	3012.4330	0.0948	0.7632
HKYI	40	-1381.7271	3012.5946	0.0874	0.8506
K2PIG	38	-1388.0629	3012.8092	0.0785	0.9292
K2PI	37	-1391.2811	3013.0171	0.0708	1.0000
GTRG	44	-1378.0049	3030.0642	0.0000	1.0000
SYMG	41	-1388.7125	3032.7939	0.0000	1.0000
GTRIG	45	-1376.2864	3032.8557	0.0000	1.0000
GTRI	44	-1379.5770	3033.2085	0.0000	1.0000
SYMIG	42	-1386.8801	3035.3577	0.0000	1.0000
SYMI	41	-1390.1900	3035.7490	0.0000	1.0000
HKY	39	-1404.1307	3051.1734	0.0000	1.0000
K2P	36	-1414.3102	3052.8467	0.0000	1.0000
GTR	43	-1401.5671	3070.9602	0.0000	1.0000
SYM	40	-1412.7302	3074.6008	0.0000	1.0000
JC69G	36	-1426.5372	3077.3007	0.0000	1.0000
F81G	39	-1418.2878	3079.4876	0.0000	1.0000
JC69I	36	-1427.9338	3080.0939	0.0000	1.0000
JC69IG	37	-1425.0893	3080.6336	0.0000	1.0000
F81I	39	-1419.7219	3082.3558	0.0000	1.0000
F81IG	40	-1416.9024	3082.9451	0.0000	1.0000
JC69	35	-1449.6154	3117.2286	0.0000	1.0000
F81	38	-1440.7378	3118.1591	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_3116.phylip = 1 - 507;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3116.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_3116.phylip = 1 - 507;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3116.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_3116.phylip = 1 - 507;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3116.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

