
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:18 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/chr11_6409.phylip" (19 taxa, 639 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2426.7625	4948.1916	0.6037	0.6037
GTRIG	45	-2426.5604	4950.1023	0.2322	0.8359
HKYG	40	-2433.0215	4951.5279	0.1139	0.9498
HKYIG	41	-2432.7407	4953.2502	0.0481	0.9979
K2PG	37	-2441.1925	4961.0639	0.0010	0.9989
K2PIG	38	-2440.8703	4962.6805	0.0004	0.9993
GTRI	44	-2434.3727	4963.4121	0.0003	0.9996
SYMG	41	-2438.1216	4964.0120	0.0002	0.9998
SYMIG	42	-2437.8738	4965.8081	0.0001	0.9999
HKYI	40	-2440.4951	4966.4752	0.0001	1.0000
K2PI	37	-2449.0830	4976.8448	0.0000	1.0000
SYMI	41	-2446.0284	4979.8256	0.0000	1.0000
GTR	43	-2473.2523	5038.8642	0.0000	1.0000
HKY	39	-2480.0577	5043.3241	0.0000	1.0000
F81G	39	-2482.1200	5047.4487	0.0000	1.0000
F81IG	40	-2481.8989	5049.2828	0.0000	1.0000
JC69G	36	-2488.6912	5053.8077	0.0000	1.0000
K2P	36	-2489.2166	5054.8584	0.0000	1.0000
SYM	40	-2484.7526	5054.9900	0.0000	1.0000
JC69IG	37	-2488.4446	5055.5680	0.0000	1.0000
F81I	39	-2489.7791	5062.7670	0.0000	1.0000
JC69I	36	-2496.5714	5069.5679	0.0000	1.0000
F81	38	-2526.3989	5133.7377	0.0000	1.0000
JC69	35	-2533.3526	5140.8844	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2426.7625	4941.5249	0.6221	0.6221
GTRIG	45	-2426.5604	4943.1209	0.2801	0.9022
HKYG	40	-2433.0215	4946.0430	0.0650	0.9672
HKYIG	41	-2432.7407	4947.4814	0.0317	0.9989
K2PG	37	-2441.1925	4956.3850	0.0004	0.9993
GTRI	44	-2434.3727	4956.7455	0.0003	0.9996
K2PIG	38	-2440.8703	4957.7405	0.0002	0.9997
SYMG	41	-2438.1216	4958.2431	0.0001	0.9999
SYMIG	42	-2437.8738	4959.7477	0.0001	1.0000
HKYI	40	-2440.4951	4960.9902	0.0000	1.0000
K2PI	37	-2449.0830	4972.1659	0.0000	1.0000
SYMI	41	-2446.0284	4974.0567	0.0000	1.0000
GTR	43	-2473.2523	5032.5045	0.0000	1.0000
HKY	39	-2480.0577	5038.1154	0.0000	1.0000
F81G	39	-2482.1200	5042.2400	0.0000	1.0000
F81IG	40	-2481.8989	5043.7979	0.0000	1.0000
JC69G	36	-2488.6912	5049.3824	0.0000	1.0000
SYM	40	-2484.7526	5049.5051	0.0000	1.0000
K2P	36	-2489.2166	5050.4332	0.0000	1.0000
JC69IG	37	-2488.4446	5050.8892	0.0000	1.0000
F81I	39	-2489.7791	5057.5583	0.0000	1.0000
JC69I	36	-2496.5714	5065.1427	0.0000	1.0000
F81	38	-2526.3989	5128.7977	0.0000	1.0000
JC69	35	-2533.3526	5136.7053	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2441.1925	5121.4015	0.7777	0.7777
HKYG	40	-2433.0215	5124.4391	0.1703	0.9480
K2PIG	38	-2440.8703	5127.2169	0.0425	0.9904
HKYIG	41	-2432.7407	5130.3375	0.0089	0.9993
K2PI	37	-2449.0830	5137.1824	0.0003	0.9996
GTRG	44	-2426.7625	5137.7607	0.0002	0.9998
HKYI	40	-2440.4951	5139.3864	0.0001	0.9999
SYMG	41	-2438.1216	5141.0992	0.0000	1.0000
GTRIG	45	-2426.5604	5143.8166	0.0000	1.0000
SYMIG	42	-2437.8738	5147.0637	0.0000	1.0000
GTRI	44	-2434.3727	5152.9813	0.0000	1.0000
SYMI	41	-2446.0284	5156.9128	0.0000	1.0000
JC69G	36	-2488.6912	5209.9390	0.0000	1.0000
K2P	36	-2489.2166	5210.9897	0.0000	1.0000
HKY	39	-2480.0577	5212.0517	0.0000	1.0000
JC69IG	37	-2488.4446	5215.9056	0.0000	1.0000
F81G	39	-2482.1200	5216.1763	0.0000	1.0000
F81IG	40	-2481.8989	5222.1940	0.0000	1.0000
GTR	43	-2473.2523	5224.2804	0.0000	1.0000
JC69I	36	-2496.5714	5225.6993	0.0000	1.0000
SYM	40	-2484.7526	5227.9013	0.0000	1.0000
F81I	39	-2489.7791	5231.4946	0.0000	1.0000
JC69	35	-2533.3526	5292.8019	0.0000	1.0000
F81	38	-2526.3989	5298.2741	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/chr11_6409.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6409.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/chr11_6409.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6409.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6409.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6409.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

