
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:47 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/chr7_11573.phylip" (19 taxa, 423 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	-1541.3426	3171.2717	0.4113	0.4113
GTRG	44	-1536.5131	3171.5025	0.3665	0.7777
GTRI	44	-1538.1484	3174.7730	0.0714	0.8492
HKYI	40	-1543.2035	3174.9935	0.0640	0.9131
GTRIG	45	-1537.3923	3175.7660	0.0435	0.9566
HKYIG	41	-1542.3654	3175.7701	0.0434	1.0000
HKY	39	-1554.7393	3195.6248	0.0000	1.0000
GTR	43	-1550.0060	3195.9963	0.0000	1.0000
K2PG	37	-1565.5732	3212.4503	0.0000	1.0000
K2PI	37	-1566.6311	3214.5661	0.0000	1.0000
K2PIG	38	-1565.4993	3214.7174	0.0000	1.0000
SYMG	41	-1564.9202	3220.8797	0.0000	1.0000
SYMI	41	-1565.8991	3222.8375	0.0000	1.0000
SYMIG	42	-1564.8445	3223.1942	0.0000	1.0000
K2P	36	-1577.6744	3234.2504	0.0000	1.0000
F81G	39	-1575.6937	3237.5337	0.0000	1.0000
F81I	39	-1577.4919	3241.1300	0.0000	1.0000
SYM	40	-1576.6793	3241.9449	0.0000	1.0000
F81IG	40	-1576.9076	3242.4017	0.0000	1.0000
F81	38	-1587.9806	3259.6800	0.0000	1.0000
JC69G	36	-1594.4553	3267.8122	0.0000	1.0000
JC69I	36	-1596.5890	3272.0796	0.0000	1.0000
JC69IG	37	-1595.7770	3272.8579	0.0000	1.0000
JC69	35	-1607.2327	3290.9771	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1536.5131	3161.0263	0.5237	0.5237
HKYG	40	-1541.3426	3162.6853	0.2285	0.7522
GTRI	44	-1538.1484	3164.2968	0.1021	0.8543
GTRIG	45	-1537.3923	3164.7846	0.0800	0.9342
HKYI	40	-1543.2035	3166.4071	0.0355	0.9698
HKYIG	41	-1542.3654	3166.7307	0.0302	1.0000
GTR	43	-1550.0060	3186.0121	0.0000	1.0000
HKY	39	-1554.7393	3187.4786	0.0000	1.0000
K2PG	37	-1565.5732	3205.1464	0.0000	1.0000
K2PIG	38	-1565.4993	3206.9986	0.0000	1.0000
K2PI	37	-1566.6311	3207.2622	0.0000	1.0000
SYMG	41	-1564.9202	3211.8403	0.0000	1.0000
SYMIG	42	-1564.8445	3213.6889	0.0000	1.0000
SYMI	41	-1565.8991	3213.7981	0.0000	1.0000
K2P	36	-1577.6744	3227.3488	0.0000	1.0000
F81G	39	-1575.6937	3229.3874	0.0000	1.0000
F81I	39	-1577.4919	3232.9838	0.0000	1.0000
SYM	40	-1576.6793	3233.3586	0.0000	1.0000
F81IG	40	-1576.9076	3233.8153	0.0000	1.0000
F81	38	-1587.9806	3251.9612	0.0000	1.0000
JC69G	36	-1594.4553	3260.9107	0.0000	1.0000
JC69I	36	-1596.5890	3265.1780	0.0000	1.0000
JC69IG	37	-1595.7770	3265.5540	0.0000	1.0000
JC69	35	-1607.2327	3284.4655	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1541.3426	3324.5802	0.8519	0.8519
HKYI	40	-1543.2035	3328.3020	0.1325	0.9844
HKYIG	41	-1542.3654	3332.6730	0.0149	0.9992
GTRG	44	-1536.5131	3339.1107	0.0006	0.9998
GTRI	44	-1538.1484	3342.3812	0.0001	1.0000
HKY	39	-1554.7393	3345.3261	0.0000	1.0000
GTRIG	45	-1537.3923	3346.9163	0.0000	1.0000
K2PG	37	-1565.5732	3354.8991	0.0000	1.0000
K2PI	37	-1566.6311	3357.0150	0.0000	1.0000
GTR	43	-1550.0060	3360.0491	0.0000	1.0000
K2PIG	38	-1565.4993	3360.7988	0.0000	1.0000
K2P	36	-1577.6744	3373.0542	0.0000	1.0000
SYMG	41	-1564.9202	3377.7826	0.0000	1.0000
SYMI	41	-1565.8991	3379.7404	0.0000	1.0000
SYMIG	42	-1564.8445	3383.6786	0.0000	1.0000
F81G	39	-1575.6937	3387.2350	0.0000	1.0000
F81I	39	-1577.4919	3390.8313	0.0000	1.0000
SYM	40	-1576.6793	3395.2534	0.0000	1.0000
F81IG	40	-1576.9076	3395.7102	0.0000	1.0000
F81	38	-1587.9806	3405.7614	0.0000	1.0000
JC69G	36	-1594.4553	3406.6161	0.0000	1.0000
JC69I	36	-1596.5890	3410.8834	0.0000	1.0000
JC69IG	37	-1595.7770	3415.3068	0.0000	1.0000
JC69	35	-1607.2327	3426.1235	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/chr7_11573.phylip = 1 - 423;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11573.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/chr7_11573.phylip = 1 - 423;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11573.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/chr7_11573.phylip = 1 - 423;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11573.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

