
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:46 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_3396.phylip" (19 taxa, 328 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-1215.1654	2532.3237	0.7655	0.7655
GTRIG	45	-1215.1180	2534.9169	0.2093	0.9748
GTRI	44	-1218.6555	2539.3039	0.0233	0.9981
HKYG	40	-1226.7842	2544.9970	0.0014	0.9995
HKYIG	41	-1226.6710	2547.3840	0.0004	0.9999
HKYI	40	-1229.2478	2549.9243	0.0001	1.0000
GTR	43	-1230.8542	2561.0323	0.0000	1.0000
SYMG	41	-1235.4510	2564.9441	0.0000	1.0000
K2PG	37	-1240.8901	2565.4767	0.0000	1.0000
SYMIG	42	-1235.2982	2567.2700	0.0000	1.0000
K2PIG	38	-1240.7110	2567.6782	0.0000	1.0000
SYMI	41	-1236.8255	2567.6930	0.0000	1.0000
K2PI	37	-1242.8695	2569.4355	0.0000	1.0000
HKY	39	-1241.7845	2572.4024	0.0000	1.0000
F81G	39	-1250.0988	2589.0309	0.0000	1.0000
F81IG	40	-1249.9791	2591.3867	0.0000	1.0000
F81I	39	-1252.1196	2593.0726	0.0000	1.0000
SYM	40	-1251.7105	2594.8495	0.0000	1.0000
K2P	36	-1257.2632	2595.6811	0.0000	1.0000
JC69G	36	-1261.3667	2603.8880	0.0000	1.0000
JC69IG	37	-1261.2124	2606.1214	0.0000	1.0000
JC69I	36	-1263.2456	2607.6459	0.0000	1.0000
F81	38	-1265.0405	2616.3370	0.0000	1.0000
JC69	35	-1277.1970	2633.0241	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1215.1654	2518.3307	0.7057	0.7057
GTRIG	45	-1215.1180	2520.2361	0.2722	0.9780
GTRI	44	-1218.6555	2525.3110	0.0215	0.9995
HKYG	40	-1226.7842	2533.5684	0.0003	0.9998
HKYIG	41	-1226.6710	2535.3421	0.0001	1.0000
HKYI	40	-1229.2478	2538.4957	0.0000	1.0000
GTR	43	-1230.8542	2547.7083	0.0000	1.0000
SYMG	41	-1235.4510	2552.9021	0.0000	1.0000
SYMIG	42	-1235.2982	2554.5963	0.0000	1.0000
SYMI	41	-1236.8255	2555.6511	0.0000	1.0000
K2PG	37	-1240.8901	2555.7801	0.0000	1.0000
K2PIG	38	-1240.7110	2557.4221	0.0000	1.0000
K2PI	37	-1242.8695	2559.7389	0.0000	1.0000
HKY	39	-1241.7845	2561.5690	0.0000	1.0000
F81G	39	-1250.0988	2578.1976	0.0000	1.0000
F81IG	40	-1249.9791	2579.9581	0.0000	1.0000
F81I	39	-1252.1196	2582.2392	0.0000	1.0000
SYM	40	-1251.7105	2583.4210	0.0000	1.0000
K2P	36	-1257.2632	2586.5265	0.0000	1.0000
JC69G	36	-1261.3667	2594.7334	0.0000	1.0000
JC69IG	37	-1261.2124	2596.4249	0.0000	1.0000
JC69I	36	-1263.2456	2598.4912	0.0000	1.0000
F81	38	-1265.0405	2606.0809	0.0000	1.0000
JC69	35	-1277.1970	2624.3940	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1215.1654	2685.2233	0.4538	0.4538
HKYG	40	-1226.7842	2685.2889	0.4392	0.8930
HKYI	40	-1229.2478	2690.2162	0.0374	0.9304
HKYIG	41	-1226.6710	2690.8556	0.0272	0.9575
GTRIG	45	-1215.1180	2690.9217	0.0263	0.9838
GTRI	44	-1218.6555	2692.2036	0.0138	0.9976
K2PG	37	-1240.8901	2696.1216	0.0020	0.9996
K2PI	37	-1242.8695	2700.0804	0.0003	0.9999
K2PIG	38	-1240.7110	2701.5566	0.0001	1.0000
SYMG	41	-1235.4510	2708.4157	0.0000	1.0000
HKY	39	-1241.7845	2709.4966	0.0000	1.0000
GTR	43	-1230.8542	2710.8079	0.0000	1.0000
SYMI	41	-1236.8255	2711.1646	0.0000	1.0000
SYMIG	42	-1235.2982	2713.9029	0.0000	1.0000
K2P	36	-1257.2632	2723.0749	0.0000	1.0000
F81G	39	-1250.0988	2726.1251	0.0000	1.0000
F81I	39	-1252.1196	2730.1668	0.0000	1.0000
JC69G	36	-1261.3667	2731.2819	0.0000	1.0000
F81IG	40	-1249.9791	2731.6787	0.0000	1.0000
JC69I	36	-1263.2456	2735.0397	0.0000	1.0000
SYM	40	-1251.7105	2735.1415	0.0000	1.0000
JC69IG	37	-1261.2124	2736.7664	0.0000	1.0000
F81	38	-1265.0405	2750.2154	0.0000	1.0000
JC69	35	-1277.1970	2757.1494	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/chr5_3396.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3396.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/chr5_3396.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3396.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3396.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3396.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;


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End of Output

