
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:43 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/chr2_10510.phylip" (19 taxa, 625 characters)

Minimum AIC  model: GTRG
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	-2833.9120	5753.4405	0.5302	0.5302
GTRG	44	-2829.7510	5754.3295	0.3400	0.8702
GTRIG	45	-2829.6921	5756.5344	0.1129	0.9831
GTRI	44	-2832.7804	5760.3883	0.0164	0.9995
HKYIG	41	-2839.9158	5767.7389	0.0004	0.9999
HKYI	40	-2843.0672	5771.7509	0.0001	1.0000
K2PG	37	-2850.1760	5779.1424	0.0000	1.0000
K2PIG	38	-2850.0553	5781.1686	0.0000	1.0000
SYMG	41	-2847.9832	5783.8737	0.0000	1.0000
K2PI	37	-2852.9139	5784.6183	0.0000	1.0000
SYMI	41	-2850.3773	5788.6620	0.0000	1.0000
SYMIG	42	-2853.4120	5797.0302	0.0000	1.0000
GTR	43	-2869.2205	5830.9538	0.0000	1.0000
HKY	39	-2878.1987	5839.7307	0.0000	1.0000
K2P	36	-2895.1823	5866.8953	0.0000	1.0000
SYM	40	-2893.2510	5872.1184	0.0000	1.0000
F81IG	40	-2905.2958	5896.2079	0.0000	1.0000
F81G	39	-2909.8703	5903.0739	0.0000	1.0000
F81I	39	-2911.1345	5905.6023	0.0000	1.0000
JC69IG	37	-2919.9807	5918.7519	0.0000	1.0000
JC69G	36	-2923.7925	5924.1157	0.0000	1.0000
JC69I	36	-2926.0944	5928.7195	0.0000	1.0000
F81	38	-2950.8793	5982.8167	0.0000	1.0000
JC69	35	-2964.9319	6004.1422	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2829.7510	5747.5019	0.4366	0.4366
HKYG	40	-2833.9120	5747.8241	0.3716	0.8082
GTRIG	45	-2829.6921	5749.3841	0.1703	0.9785
GTRI	44	-2832.7804	5753.5607	0.0211	0.9996
HKYIG	41	-2839.9158	5761.8315	0.0003	1.0000
HKYI	40	-2843.0672	5766.1345	0.0000	1.0000
K2PG	37	-2850.1760	5774.3520	0.0000	1.0000
K2PIG	38	-2850.0553	5776.1106	0.0000	1.0000
SYMG	41	-2847.9832	5777.9664	0.0000	1.0000
K2PI	37	-2852.9139	5779.8278	0.0000	1.0000
SYMI	41	-2850.3773	5782.7546	0.0000	1.0000
SYMIG	42	-2853.4120	5790.8240	0.0000	1.0000
GTR	43	-2869.2205	5824.4409	0.0000	1.0000
HKY	39	-2878.1987	5834.3973	0.0000	1.0000
K2P	36	-2895.1823	5862.3646	0.0000	1.0000
SYM	40	-2893.2510	5866.5020	0.0000	1.0000
F81IG	40	-2905.2958	5890.5915	0.0000	1.0000
F81G	39	-2909.8703	5897.7406	0.0000	1.0000
F81I	39	-2911.1345	5900.2689	0.0000	1.0000
JC69IG	37	-2919.9807	5913.9615	0.0000	1.0000
JC69G	36	-2923.7925	5919.5850	0.0000	1.0000
JC69I	36	-2926.0944	5924.1888	0.0000	1.0000
F81	38	-2950.8793	5977.7587	0.0000	1.0000
JC69	35	-2964.9319	5999.8638	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2833.9120	5925.3342	0.9981	0.9981
K2PG	37	-2850.1760	5938.5488	0.0013	0.9995
GTRG	44	-2829.7510	5942.7630	0.0002	0.9996
HKYI	40	-2843.0672	5943.6445	0.0001	0.9997
HKYIG	41	-2839.9158	5943.7793	0.0001	0.9998
K2PI	37	-2852.9139	5944.0247	0.0001	0.9999
K2PIG	38	-2850.0553	5944.7452	0.0001	1.0000
GTRI	44	-2832.7804	5948.8218	0.0000	1.0000
GTRIG	45	-2829.6921	5949.0830	0.0000	1.0000
SYMG	41	-2847.9832	5959.9142	0.0000	1.0000
SYMI	41	-2850.3773	5964.7024	0.0000	1.0000
SYMIG	42	-2853.4120	5977.2096	0.0000	1.0000
HKY	39	-2878.1987	6007.4697	0.0000	1.0000
GTR	43	-2869.2205	6015.2642	0.0000	1.0000
K2P	36	-2895.1823	6022.1237	0.0000	1.0000
SYM	40	-2893.2510	6044.0121	0.0000	1.0000
F81IG	40	-2905.2958	6068.1016	0.0000	1.0000
F81G	39	-2909.8703	6070.8129	0.0000	1.0000
F81I	39	-2911.1345	6073.3412	0.0000	1.0000
JC69IG	37	-2919.9807	6078.1583	0.0000	1.0000
JC69G	36	-2923.7925	6079.3441	0.0000	1.0000
JC69I	36	-2926.0944	6083.9479	0.0000	1.0000
F81	38	-2950.8793	6146.3932	0.0000	1.0000
JC69	35	-2964.9319	6155.1851	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/chr2_10510.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_10510.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/chr2_10510.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_10510.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/chr2_10510.phylip = 1 - 625;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_10510.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

