
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:21 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/chr5_11156.phylip" (19 taxa, 388 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1250.5909	2600.7270	0.3682	0.3682
GTRG	44	-1250.6717	2600.8886	0.3396	0.7078
HKYI	40	-1256.9651	2603.3827	0.0976	0.8054
GTRIG	45	-1250.6714	2603.4481	0.0945	0.8999
HKYG	40	-1257.1790	2603.8104	0.0788	0.9787
HKYIG	41	-1257.2380	2606.4297	0.0213	1.0000
GTR	43	-1261.4854	2619.9708	0.0000	1.0000
HKY	39	-1268.0879	2623.1414	0.0000	1.0000
K2PI	37	-1271.9613	2625.9568	0.0000	1.0000
SYMI	41	-1267.1609	2626.2755	0.0000	1.0000
K2PG	37	-1272.3713	2626.7768	0.0000	1.0000
SYMG	41	-1267.5194	2626.9926	0.0000	1.0000
K2PIG	38	-1272.4501	2629.3930	0.0000	1.0000
SYMIG	42	-1267.5191	2629.5078	0.0000	1.0000
SYM	40	-1278.4093	2646.2710	0.0000	1.0000
K2P	36	-1283.6195	2646.8288	0.0000	1.0000
F81I	39	-1291.3599	2669.6853	0.0000	1.0000
F81G	39	-1291.8219	2670.6094	0.0000	1.0000
F81IG	40	-1291.3723	2672.1971	0.0000	1.0000
JC69I	36	-1303.7518	2687.0934	0.0000	1.0000
JC69G	36	-1304.2877	2688.1651	0.0000	1.0000
F81	38	-1301.8463	2688.1854	0.0000	1.0000
JC69IG	37	-1304.3504	2690.7350	0.0000	1.0000
JC69	35	-1314.6727	2706.5045	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1250.5909	2589.1818	0.4071	0.4071
GTRG	44	-1250.6717	2589.3434	0.3755	0.7827
GTRIG	45	-1250.6714	2591.3428	0.1382	0.9209
HKYI	40	-1256.9651	2593.9303	0.0379	0.9588
HKYG	40	-1257.1790	2594.3580	0.0306	0.9894
HKYIG	41	-1257.2380	2596.4759	0.0106	1.0000
GTR	43	-1261.4854	2608.9708	0.0000	1.0000
HKY	39	-1268.0879	2614.1759	0.0000	1.0000
SYMI	41	-1267.1609	2616.3217	0.0000	1.0000
SYMG	41	-1267.5194	2617.0389	0.0000	1.0000
K2PI	37	-1271.9613	2617.9226	0.0000	1.0000
K2PG	37	-1272.3713	2618.7425	0.0000	1.0000
SYMIG	42	-1267.5191	2619.0382	0.0000	1.0000
K2PIG	38	-1272.4501	2620.9002	0.0000	1.0000
SYM	40	-1278.4093	2636.8185	0.0000	1.0000
K2P	36	-1283.6195	2639.2390	0.0000	1.0000
F81I	39	-1291.3599	2660.7198	0.0000	1.0000
F81G	39	-1291.8219	2661.6438	0.0000	1.0000
F81IG	40	-1291.3723	2662.7446	0.0000	1.0000
JC69I	36	-1303.7518	2679.5036	0.0000	1.0000
F81	38	-1301.8463	2679.6925	0.0000	1.0000
JC69G	36	-1304.2877	2680.5753	0.0000	1.0000
JC69IG	37	-1304.3504	2682.7008	0.0000	1.0000
JC69	35	-1314.6727	2699.3454	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1256.9651	2752.3705	0.5382	0.5382
HKYG	40	-1257.1790	2752.7982	0.4346	0.9728
HKYIG	41	-1257.2380	2758.8772	0.0208	0.9936
GTRI	44	-1250.5909	2763.4661	0.0021	0.9957
GTRG	44	-1250.6717	2763.6277	0.0019	0.9976
K2PI	37	-1271.9613	2764.4798	0.0013	0.9989
K2PG	37	-1272.3713	2765.2997	0.0008	0.9997
HKY	39	-1268.0879	2768.6551	0.0002	0.9999
GTRIG	45	-1250.6714	2769.5881	0.0001	1.0000
K2PIG	38	-1272.4501	2771.4184	0.0000	1.0000
SYMI	41	-1267.1609	2778.7229	0.0000	1.0000
GTR	43	-1261.4854	2779.2940	0.0000	1.0000
SYMG	41	-1267.5194	2779.4401	0.0000	1.0000
K2P	36	-1283.6195	2781.8352	0.0000	1.0000
SYMIG	42	-1267.5191	2785.4005	0.0000	1.0000
SYM	40	-1278.4093	2795.2587	0.0000	1.0000
F81I	39	-1291.3599	2815.1990	0.0000	1.0000
F81G	39	-1291.8219	2816.1230	0.0000	1.0000
F81IG	40	-1291.3723	2821.1849	0.0000	1.0000
JC69I	36	-1303.7518	2822.0998	0.0000	1.0000
JC69G	36	-1304.2877	2823.1715	0.0000	1.0000
JC69IG	37	-1304.3504	2829.2580	0.0000	1.0000
F81	38	-1301.8463	2830.2107	0.0000	1.0000
JC69	35	-1314.6727	2837.9806	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip = 1 - 388;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip = 1 - 388;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip = 1 - 388;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11156.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

