
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:53 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/chr2_27234.phylip" (19 taxa, 446 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	-1217.1495	2532.1743	0.3112	0.3112
GTRI	44	-1217.4540	2532.7833	0.2295	0.5406
HKYG	40	-1222.7616	2533.6221	0.1509	0.6915
GTRIG	45	-1216.7748	2533.8995	0.1313	0.8228
HKYI	40	-1222.9866	2534.0719	0.1205	0.9433
HKYIG	41	-1222.5279	2535.5805	0.0567	1.0000
K2PG	37	-1235.3060	2551.5043	0.0000	1.0000
K2PI	37	-1235.5474	2551.9870	0.0000	1.0000
K2PIG	38	-1235.0742	2553.4310	0.0000	1.0000
SYMG	41	-1233.3076	2557.1400	0.0000	1.0000
SYMI	41	-1233.5759	2557.6765	0.0000	1.0000
SYMIG	42	-1233.0345	2559.0318	0.0000	1.0000
F81G	39	-1237.7803	2561.2454	0.0000	1.0000
F81I	39	-1237.9280	2561.5407	0.0000	1.0000
F81IG	40	-1237.7181	2563.5349	0.0000	1.0000
GTR	43	-1237.8659	2571.1447	0.0000	1.0000
HKY	39	-1243.7987	2573.2821	0.0000	1.0000
JC69G	36	-1248.9787	2576.4707	0.0000	1.0000
JC69I	36	-1249.1514	2576.8163	0.0000	1.0000
JC69IG	37	-1248.8078	2578.5078	0.0000	1.0000
K2P	36	-1257.5209	2593.5552	0.0000	1.0000
SYM	40	-1254.8155	2597.7298	0.0000	1.0000
F81	38	-1258.4987	2600.2799	0.0000	1.0000
JC69	35	-1270.4968	2617.1399	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1217.1495	2522.2990	0.3671	0.3671
GTRI	44	-1217.4540	2522.9080	0.2707	0.6378
GTRIG	45	-1216.7748	2523.5495	0.1964	0.8343
HKYG	40	-1222.7616	2525.5233	0.0732	0.9075
HKYI	40	-1222.9866	2525.9732	0.0585	0.9660
HKYIG	41	-1222.5279	2527.0558	0.0340	1.0000
K2PG	37	-1235.3060	2544.6121	0.0000	1.0000
K2PI	37	-1235.5474	2545.0948	0.0000	1.0000
K2PIG	38	-1235.0742	2546.1485	0.0000	1.0000
SYMG	41	-1233.3076	2548.6153	0.0000	1.0000
SYMI	41	-1233.5759	2549.1518	0.0000	1.0000
SYMIG	42	-1233.0345	2550.0690	0.0000	1.0000
F81G	39	-1237.7803	2553.5607	0.0000	1.0000
F81I	39	-1237.9280	2553.8560	0.0000	1.0000
F81IG	40	-1237.7181	2555.4362	0.0000	1.0000
GTR	43	-1237.8659	2561.7318	0.0000	1.0000
HKY	39	-1243.7987	2565.5974	0.0000	1.0000
JC69G	36	-1248.9787	2569.9573	0.0000	1.0000
JC69I	36	-1249.1514	2570.3028	0.0000	1.0000
JC69IG	37	-1248.8078	2571.6156	0.0000	1.0000
K2P	36	-1257.5209	2587.0418	0.0000	1.0000
SYM	40	-1254.8155	2589.6310	0.0000	1.0000
F81	38	-1258.4987	2592.9974	0.0000	1.0000
JC69	35	-1270.4968	2610.9935	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1222.7616	2689.5361	0.5201	0.5201
HKYI	40	-1222.9866	2689.9859	0.4153	0.9354
HKYIG	41	-1222.5279	2695.1688	0.0311	0.9665
K2PG	37	-1235.3060	2696.3239	0.0175	0.9839
K2PI	37	-1235.5474	2696.8066	0.0137	0.9977
K2PIG	38	-1235.0742	2701.9606	0.0010	0.9987
GTRG	44	-1217.1495	2702.7130	0.0007	0.9994
GTRI	44	-1217.4540	2703.3221	0.0005	0.9999
GTRIG	45	-1216.7748	2708.0639	0.0000	1.0000
F81G	39	-1237.7803	2713.4731	0.0000	1.0000
F81I	39	-1237.9280	2713.7684	0.0000	1.0000
SYMG	41	-1233.3076	2716.7284	0.0000	1.0000
SYMI	41	-1233.5759	2717.2649	0.0000	1.0000
JC69G	36	-1248.9787	2717.5688	0.0000	1.0000
JC69I	36	-1249.1514	2717.9143	0.0000	1.0000
F81IG	40	-1237.7181	2719.4489	0.0000	1.0000
SYMIG	42	-1233.0345	2722.2824	0.0000	1.0000
JC69IG	37	-1248.8078	2723.3274	0.0000	1.0000
HKY	39	-1243.7987	2725.5098	0.0000	1.0000
K2P	36	-1257.5209	2734.6533	0.0000	1.0000
GTR	43	-1237.8659	2738.0455	0.0000	1.0000
F81	38	-1258.4987	2748.8095	0.0000	1.0000
SYM	40	-1254.8155	2753.6438	0.0000	1.0000
JC69	35	-1270.4968	2754.5047	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/chr2_27234.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27234.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/chr2_27234.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27234.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/chr2_27234.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27234.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

