
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:05 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/chr10_4790.phylip" (19 taxa, 378 characters)

Minimum AIC  model: GTRG
Minimum AICc model: K2PG
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
K2PG	37	-1510.9879	3104.2463	0.2438	0.2438
HKYI	40	-1507.3428	3104.4185	0.2237	0.4676
HKYG	40	-1507.4876	3104.7081	0.1936	0.6611
HKYIG	41	-1506.5275	3105.3049	0.1436	0.8047
GTRG	44	-1503.1674	3106.2266	0.0906	0.8953
K2PI	37	-1512.8161	3107.9027	0.0392	0.9345
GTRIG	45	-1502.9196	3108.3091	0.0320	0.9665
K2PIG	38	-1511.9291	3108.6015	0.0276	0.9941
GTRI	44	-1506.1095	3112.1109	0.0048	0.9989
SYMG	41	-1511.7241	3115.6982	0.0008	0.9997
SYMIG	42	-1511.5157	3117.8135	0.0003	1.0000
SYMI	41	-1515.2253	3122.7006	0.0000	1.0000
F81G	39	-1549.2241	3185.6790	0.0000	1.0000
HKY	39	-1549.9670	3187.1648	0.0000	1.0000
K2P	36	-1555.1644	3190.1410	0.0000	1.0000
F81IG	40	-1550.8053	3191.3436	0.0000	1.0000
F81I	39	-1553.1026	3193.4359	0.0000	1.0000
GTR	43	-1549.2595	3195.8484	0.0000	1.0000
JC69G	36	-1558.5267	3196.8657	0.0000	1.0000
JC69IG	37	-1559.4988	3201.2682	0.0000	1.0000
JC69I	36	-1561.6757	3203.1637	0.0000	1.0000
SYM	40	-1558.1399	3206.0127	0.0000	1.0000
F81	38	-1587.6040	3259.9514	0.0000	1.0000
JC69	35	-1596.6706	3270.7096	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1503.1674	3094.3347	0.2290	0.2290
HKYI	40	-1507.3428	3094.6856	0.1922	0.4212
HKYG	40	-1507.4876	3094.9752	0.1663	0.5874
HKYIG	41	-1506.5275	3095.0549	0.1598	0.7472
GTRIG	45	-1502.9196	3095.8392	0.1079	0.8551
K2PG	37	-1510.9879	3095.9757	0.1008	0.9559
K2PI	37	-1512.8161	3099.6322	0.0162	0.9721
K2PIG	38	-1511.9291	3099.8582	0.0145	0.9866
GTRI	44	-1506.1095	3100.2190	0.0121	0.9987
SYMG	41	-1511.7241	3105.4482	0.0009	0.9996
SYMIG	42	-1511.5157	3107.0314	0.0004	1.0000
SYMI	41	-1515.2253	3112.4506	0.0000	1.0000
F81G	39	-1549.2241	3176.4483	0.0000	1.0000
HKY	39	-1549.9670	3177.9340	0.0000	1.0000
F81IG	40	-1550.8053	3181.6106	0.0000	1.0000
K2P	36	-1555.1644	3182.3287	0.0000	1.0000
F81I	39	-1553.1026	3184.2051	0.0000	1.0000
GTR	43	-1549.2595	3184.5191	0.0000	1.0000
JC69G	36	-1558.5267	3189.0534	0.0000	1.0000
JC69IG	37	-1559.4988	3192.9976	0.0000	1.0000
JC69I	36	-1561.6757	3195.3514	0.0000	1.0000
SYM	40	-1558.1399	3196.2797	0.0000	1.0000
F81	38	-1587.6040	3251.2081	0.0000	1.0000
JC69	35	-1596.6706	3263.3412	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1510.9879	3241.5668	0.8396	0.8396
K2PI	37	-1512.8161	3245.2232	0.1349	0.9745
K2PIG	38	-1511.9291	3249.3842	0.0168	0.9913
HKYI	40	-1507.3428	3252.0813	0.0044	0.9957
HKYG	40	-1507.4876	3252.3709	0.0038	0.9995
HKYIG	41	-1506.5275	3256.3856	0.0005	1.0000
SYMG	41	-1511.7241	3266.7789	0.0000	1.0000
GTRG	44	-1503.1674	3267.4701	0.0000	1.0000
SYMIG	42	-1511.5157	3272.2970	0.0000	1.0000
GTRIG	45	-1502.9196	3272.9095	0.0000	1.0000
GTRI	44	-1506.1095	3273.3543	0.0000	1.0000
SYMI	41	-1515.2253	3273.7813	0.0000	1.0000
K2P	36	-1555.1644	3323.9849	0.0000	1.0000
F81G	39	-1549.2241	3329.9092	0.0000	1.0000
JC69G	36	-1558.5267	3330.7096	0.0000	1.0000
HKY	39	-1549.9670	3331.3949	0.0000	1.0000
JC69I	36	-1561.6757	3337.0076	0.0000	1.0000
F81I	39	-1553.1026	3337.6660	0.0000	1.0000
JC69IG	37	-1559.4988	3338.5887	0.0000	1.0000
F81IG	40	-1550.8053	3339.0064	0.0000	1.0000
SYM	40	-1558.1399	3353.6755	0.0000	1.0000
GTR	43	-1549.2595	3353.7196	0.0000	1.0000
F81	38	-1587.6040	3400.7340	0.0000	1.0000
JC69	35	-1596.6706	3401.0625	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/chr10_4790.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4790.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4790.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4790.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;


[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/chr10_4790.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4790.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

