
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:31 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/chrZ_1330.phylip" (19 taxa, 401 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	-1189.4309	2477.9854	0.6354	0.6354
GTRIG	45	-1189.3327	2480.3273	0.1970	0.8324
GTRI	44	-1190.9291	2480.9818	0.1420	0.9744
HKYG	40	-1198.1323	2485.3756	0.0158	0.9902
HKYIG	41	-1197.9378	2487.4690	0.0055	0.9957
HKYI	40	-1199.4327	2487.9765	0.0043	1.0000
HKY	39	-1213.9945	2514.6317	0.0000	1.0000
GTR	43	-1209.6590	2515.9174	0.0000	1.0000
K2PG	37	-1220.4277	2522.6019	0.0000	1.0000
K2PIG	38	-1220.0585	2524.3049	0.0000	1.0000
K2PI	37	-1221.6995	2525.1455	0.0000	1.0000
SYMG	41	-1221.0109	2533.6151	0.0000	1.0000
SYMIG	42	-1220.6476	2535.3846	0.0000	1.0000
SYMI	41	-1222.6324	2536.8580	0.0000	1.0000
F81G	39	-1229.7723	2546.1872	0.0000	1.0000
F81IG	40	-1229.5406	2548.1923	0.0000	1.0000
F81I	39	-1230.9806	2548.6040	0.0000	1.0000
K2P	36	-1239.2139	2557.7464	0.0000	1.0000
SYM	40	-1238.4873	2566.0858	0.0000	1.0000
JC69G	36	-1248.2658	2575.8503	0.0000	1.0000
F81	38	-1246.1894	2576.5666	0.0000	1.0000
JC69IG	37	-1247.9398	2577.6262	0.0000	1.0000
JC69I	36	-1249.5477	2578.4142	0.0000	1.0000
JC69	35	-1266.4931	2609.8903	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1189.4309	2466.8618	0.6079	0.6079
GTRIG	45	-1189.3327	2468.6653	0.2467	0.8546
GTRI	44	-1190.9291	2469.8582	0.1359	0.9905
HKYG	40	-1198.1323	2476.2645	0.0055	0.9960
HKYIG	41	-1197.9378	2477.8756	0.0025	0.9985
HKYI	40	-1199.4327	2478.8654	0.0015	1.0000
GTR	43	-1209.6590	2505.3180	0.0000	1.0000
HKY	39	-1213.9945	2505.9891	0.0000	1.0000
K2PG	37	-1220.4277	2514.8553	0.0000	1.0000
K2PIG	38	-1220.0585	2516.1170	0.0000	1.0000
K2PI	37	-1221.6995	2517.3989	0.0000	1.0000
SYMG	41	-1221.0109	2524.0217	0.0000	1.0000
SYMIG	42	-1220.6476	2525.2952	0.0000	1.0000
SYMI	41	-1222.6324	2527.2647	0.0000	1.0000
F81G	39	-1229.7723	2537.5445	0.0000	1.0000
F81IG	40	-1229.5406	2539.0812	0.0000	1.0000
F81I	39	-1230.9806	2539.9613	0.0000	1.0000
K2P	36	-1239.2139	2550.4277	0.0000	1.0000
SYM	40	-1238.4873	2556.9747	0.0000	1.0000
F81	38	-1246.1894	2568.3787	0.0000	1.0000
JC69G	36	-1248.2658	2568.5316	0.0000	1.0000
JC69IG	37	-1247.9398	2569.8796	0.0000	1.0000
JC69I	36	-1249.5477	2571.0955	0.0000	1.0000
JC69	35	-1266.4931	2602.9862	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1198.1323	2636.0230	0.7242	0.7242
HKYI	40	-1199.4327	2638.6239	0.1973	0.9215
HKYIG	41	-1197.9378	2641.6281	0.0439	0.9654
GTRG	44	-1189.4309	2642.5961	0.0271	0.9925
GTRI	44	-1190.9291	2645.5925	0.0061	0.9985
GTRIG	45	-1189.3327	2648.3936	0.0015	1.0000
HKY	39	-1213.9945	2661.7536	0.0000	1.0000
K2PG	37	-1220.4277	2662.6319	0.0000	1.0000
K2PI	37	-1221.6995	2665.1755	0.0000	1.0000
K2PIG	38	-1220.0585	2667.8876	0.0000	1.0000
GTR	43	-1209.6590	2677.0583	0.0000	1.0000
SYMG	41	-1221.0109	2687.7742	0.0000	1.0000
SYMI	41	-1222.6324	2691.0171	0.0000	1.0000
SYMIG	42	-1220.6476	2693.0416	0.0000	1.0000
F81G	39	-1229.7723	2693.3090	0.0000	1.0000
K2P	36	-1239.2139	2694.2103	0.0000	1.0000
F81I	39	-1230.9806	2695.7258	0.0000	1.0000
F81IG	40	-1229.5406	2698.8397	0.0000	1.0000
JC69G	36	-1248.2658	2712.3142	0.0000	1.0000
JC69I	36	-1249.5477	2714.8781	0.0000	1.0000
SYM	40	-1238.4873	2716.7331	0.0000	1.0000
JC69IG	37	-1247.9398	2717.6562	0.0000	1.0000
F81	38	-1246.1894	2720.1493	0.0000	1.0000
JC69	35	-1266.4931	2742.7748	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/chrZ_1330.phylip = 1 - 401;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_1330.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/chrZ_1330.phylip = 1 - 401;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_1330.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/chrZ_1330.phylip = 1 - 401;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_1330.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

