
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:49 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_3405.phylip" (19 taxa, 1068 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2756.5382	5596.2702	0.3609	0.3609
HKYI	40	-2757.1377	5597.4691	0.1982	0.5591
GTRG	44	-2753.0227	5597.9163	0.1585	0.7176
HKYIG	41	-2756.3688	5598.0942	0.1450	0.8625
GTRI	44	-2753.8539	5599.5787	0.0690	0.9316
GTRIG	45	-2752.7723	5599.5954	0.0684	1.0000
K2PG	37	-2777.5622	5631.8546	0.0000	1.0000
K2PI	37	-2777.8937	5632.5175	0.0000	1.0000
K2PIG	38	-2777.5066	5633.8937	0.0000	1.0000
SYMG	41	-2776.2621	5637.8809	0.0000	1.0000
SYMI	41	-2776.6331	5638.6229	0.0000	1.0000
SYMIG	42	-2776.1933	5639.9104	0.0000	1.0000
HKY	39	-2785.8090	5652.6531	0.0000	1.0000
GTR	43	-2782.1800	5654.0552	0.0000	1.0000
K2P	36	-2807.2613	5689.1064	0.0000	1.0000
SYM	40	-2805.4605	5694.1148	0.0000	1.0000
F81G	39	-2817.1360	5715.3070	0.0000	1.0000
F81I	39	-2817.4406	5715.9163	0.0000	1.0000
F81IG	40	-2817.0892	5717.3721	0.0000	1.0000
JC69G	36	-2835.2060	5744.9960	0.0000	1.0000
JC69I	36	-2835.3774	5745.3388	0.0000	1.0000
JC69IG	37	-2835.2075	5747.1451	0.0000	1.0000
F81	38	-2844.1662	5767.2129	0.0000	1.0000
JC69	35	-2862.5749	5797.5917	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2756.5382	5593.0764	0.3164	0.3164
GTRG	44	-2753.0227	5594.0454	0.1949	0.5113
HKYI	40	-2757.1377	5594.2753	0.1738	0.6851
HKYIG	41	-2756.3688	5594.7375	0.1379	0.8230
GTRIG	45	-2752.7723	5595.5445	0.0921	0.9151
GTRI	44	-2753.8539	5595.7078	0.0849	1.0000
K2PG	37	-2777.5622	5629.1245	0.0000	1.0000
K2PI	37	-2777.8937	5629.7874	0.0000	1.0000
K2PIG	38	-2777.5066	5631.0133	0.0000	1.0000
SYMG	41	-2776.2621	5634.5241	0.0000	1.0000
SYMI	41	-2776.6331	5635.2662	0.0000	1.0000
SYMIG	42	-2776.1933	5636.3865	0.0000	1.0000
HKY	39	-2785.8090	5649.6180	0.0000	1.0000
GTR	43	-2782.1800	5650.3599	0.0000	1.0000
K2P	36	-2807.2613	5686.5225	0.0000	1.0000
SYM	40	-2805.4605	5690.9210	0.0000	1.0000
F81G	39	-2817.1360	5712.2719	0.0000	1.0000
F81I	39	-2817.4406	5712.8813	0.0000	1.0000
F81IG	40	-2817.0892	5714.1784	0.0000	1.0000
JC69G	36	-2835.2060	5742.4121	0.0000	1.0000
JC69I	36	-2835.3774	5742.7549	0.0000	1.0000
JC69IG	37	-2835.2075	5744.4150	0.0000	1.0000
F81	38	-2844.1662	5764.3324	0.0000	1.0000
JC69	35	-2862.5749	5795.1498	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2756.5382	5792.0182	0.6307	0.6307
HKYI	40	-2757.1377	5793.2170	0.3463	0.9771
HKYIG	41	-2756.3688	5798.6528	0.0229	0.9999
GTRG	44	-2753.0227	5812.8813	0.0000	1.0000
K2PG	37	-2777.5622	5813.1456	0.0000	1.0000
K2PI	37	-2777.8937	5813.8085	0.0000	1.0000
GTRI	44	-2753.8539	5814.5437	0.0000	1.0000
GTRIG	45	-2752.7723	5819.3540	0.0000	1.0000
K2PIG	38	-2777.5066	5820.0079	0.0000	1.0000
SYMG	41	-2776.2621	5838.4394	0.0000	1.0000
SYMI	41	-2776.6331	5839.1815	0.0000	1.0000
HKY	39	-2785.8090	5843.5862	0.0000	1.0000
SYMIG	42	-2776.1933	5845.2753	0.0000	1.0000
GTR	43	-2782.1800	5864.2222	0.0000	1.0000
K2P	36	-2807.2613	5865.5701	0.0000	1.0000
SYM	40	-2805.4605	5889.8627	0.0000	1.0000
F81G	39	-2817.1360	5906.2401	0.0000	1.0000
F81I	39	-2817.4406	5906.8494	0.0000	1.0000
F81IG	40	-2817.0892	5913.1201	0.0000	1.0000
JC69G	36	-2835.2060	5921.4596	0.0000	1.0000
JC69I	36	-2835.3774	5921.8024	0.0000	1.0000
JC69IG	37	-2835.2075	5928.4361	0.0000	1.0000
F81	38	-2844.1662	5953.3271	0.0000	1.0000
JC69	35	-2862.5749	5969.2238	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3405.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

