
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:12 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_10013.phylip" (19 taxa, 385 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-1194.7750	2479.0850	0.3480	0.3480
HKYI	40	-1195.3732	2480.2813	0.1913	0.5393
GTRG	44	-1190.4086	2480.4643	0.1746	0.7139
HKYIG	41	-1194.6881	2481.4170	0.1084	0.8223
GTRI	44	-1191.2640	2482.1750	0.0742	0.8965
GTRIG	45	-1190.2640	2482.7404	0.0559	0.9525
SYMG	41	-1196.6256	2485.2921	0.0156	0.9681
K2PG	37	-1202.0140	2486.1318	0.0103	0.9783
SYMI	41	-1197.3773	2486.7954	0.0074	0.9857
K2PI	37	-1202.5017	2487.1072	0.0063	0.9920
SYMIG	42	-1196.5301	2487.6216	0.0049	0.9969
K2PIG	38	-1201.9750	2488.5164	0.0031	1.0000
GTR	43	-1210.2821	2517.6610	0.0000	1.0000
HKY	39	-1215.3799	2517.8034	0.0000	1.0000
SYM	40	-1215.7354	2521.0056	0.0000	1.0000
K2P	36	-1221.7891	2523.2333	0.0000	1.0000
F81G	39	-1226.7964	2540.6364	0.0000	1.0000
F81I	39	-1227.0159	2541.0753	0.0000	1.0000
F81IG	40	-1226.7989	2543.1326	0.0000	1.0000
JC69G	36	-1232.2665	2544.1883	0.0000	1.0000
JC69I	36	-1232.4961	2544.6474	0.0000	1.0000
JC69IG	37	-1232.2674	2546.6385	0.0000	1.0000
F81	38	-1246.5622	2577.6910	0.0000	1.0000
JC69	35	-1251.5612	2580.3431	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1190.4086	2468.8172	0.3032	0.3032
HKYG	40	-1194.7750	2469.5501	0.2102	0.5134
GTRI	44	-1191.2640	2470.5279	0.1289	0.6423
GTRIG	45	-1190.2640	2470.5280	0.1289	0.7712
HKYI	40	-1195.3732	2470.7464	0.1156	0.8868
HKYIG	41	-1194.6881	2471.3761	0.0844	0.9711
SYMG	41	-1196.6256	2475.2513	0.0122	0.9833
SYMI	41	-1197.3773	2476.7546	0.0057	0.9890
SYMIG	42	-1196.5301	2477.0602	0.0049	0.9939
K2PG	37	-1202.0140	2478.0281	0.0030	0.9970
K2PI	37	-1202.5017	2479.0035	0.0019	0.9988
K2PIG	38	-1201.9750	2479.9499	0.0012	1.0000
GTR	43	-1210.2821	2506.5642	0.0000	1.0000
HKY	39	-1215.3799	2508.7599	0.0000	1.0000
SYM	40	-1215.7354	2511.4707	0.0000	1.0000
K2P	36	-1221.7891	2515.5781	0.0000	1.0000
F81G	39	-1226.7964	2531.5929	0.0000	1.0000
F81I	39	-1227.0159	2532.0318	0.0000	1.0000
F81IG	40	-1226.7989	2533.5977	0.0000	1.0000
JC69G	36	-1232.2665	2536.5331	0.0000	1.0000
JC69I	36	-1232.4961	2536.9922	0.0000	1.0000
JC69IG	37	-1232.2674	2538.5347	0.0000	1.0000
F81	38	-1246.5622	2569.1245	0.0000	1.0000
JC69	35	-1251.5612	2573.1225	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1202.0140	2624.2981	0.5088	0.5088
K2PI	37	-1202.5017	2625.2735	0.3124	0.8212
HKYG	40	-1194.7750	2627.6798	0.0938	0.9150
HKYI	40	-1195.3732	2628.8761	0.0516	0.9666
K2PIG	38	-1201.9750	2630.1732	0.0270	0.9936
HKYIG	41	-1194.6881	2633.4591	0.0052	0.9988
SYMG	41	-1196.6256	2637.3342	0.0008	0.9995
SYMI	41	-1197.3773	2638.8376	0.0004	0.9999
GTRG	44	-1190.4086	2642.7599	0.0000	0.9999
SYMIG	42	-1196.5301	2643.0964	0.0000	1.0000
GTRI	44	-1191.2640	2644.4706	0.0000	1.0000
GTRIG	45	-1190.2640	2648.4239	0.0000	1.0000
K2P	36	-1221.7891	2657.8949	0.0000	1.0000
HKY	39	-1215.3799	2662.9364	0.0000	1.0000
SYM	40	-1215.7354	2669.6005	0.0000	1.0000
GTR	43	-1210.2821	2676.5537	0.0000	1.0000
JC69G	36	-1232.2665	2678.8498	0.0000	1.0000
JC69I	36	-1232.4961	2679.3090	0.0000	1.0000
JC69IG	37	-1232.2674	2684.8047	0.0000	1.0000
F81G	39	-1226.7964	2685.7694	0.0000	1.0000
F81I	39	-1227.0159	2686.2083	0.0000	1.0000
F81IG	40	-1226.7989	2691.7275	0.0000	1.0000
JC69	35	-1251.5612	2711.4860	0.0000	1.0000
F81	38	-1246.5622	2719.3477	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_10013.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_10013.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_10013.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_10013.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;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_10013.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_10013.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

