
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:54 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_9078.phylip" (19 taxa, 421 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	-1512.5848	3123.7016	0.6674	0.6674
GTRIG	45	-1512.0865	3125.2131	0.3135	0.9808
GTRI	44	-1516.1923	3130.9166	0.0181	0.9989
SYMG	41	-1523.5951	3138.2773	0.0005	0.9994
SYMIG	42	-1523.0457	3139.6469	0.0002	0.9996
HKYG	40	-1525.5531	3139.7378	0.0002	0.9999
HKYIG	41	-1525.3057	3141.6985	0.0001	0.9999
HKYI	40	-1527.6519	3143.9353	0.0000	1.0000
SYMI	41	-1526.4758	3144.0387	0.0000	1.0000
K2PG	37	-1532.6111	3146.5643	0.0000	1.0000
K2PIG	38	-1532.2910	3148.3412	0.0000	1.0000
K2PI	37	-1534.9184	3151.1789	0.0000	1.0000
GTR	43	-1551.1724	3198.3820	0.0000	1.0000
SYM	40	-1562.4314	3213.4943	0.0000	1.0000
HKY	39	-1564.3499	3214.8887	0.0000	1.0000
K2P	36	-1571.9252	3222.7878	0.0000	1.0000
F81G	39	-1571.1246	3228.4381	0.0000	1.0000
F81IG	40	-1570.8150	3230.2615	0.0000	1.0000
F81I	39	-1574.4133	3235.0155	0.0000	1.0000
JC69G	36	-1578.3459	3235.6292	0.0000	1.0000
JC69IG	37	-1578.0415	3237.4250	0.0000	1.0000
JC69I	36	-1581.8873	3242.7121	0.0000	1.0000
F81	38	-1605.9014	3295.5620	0.0000	1.0000
JC69	35	-1614.0939	3304.7334	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1512.5848	3113.1697	0.6122	0.6122
GTRIG	45	-1512.0865	3114.1731	0.3707	0.9829
GTRI	44	-1516.1923	3120.3847	0.0166	0.9995
SYMG	41	-1523.5951	3129.1902	0.0002	0.9997
SYMIG	42	-1523.0457	3130.0913	0.0001	0.9999
HKYG	40	-1525.5531	3131.1063	0.0001	0.9999
HKYIG	41	-1525.3057	3132.6114	0.0000	1.0000
SYMI	41	-1526.4758	3134.9516	0.0000	1.0000
HKYI	40	-1527.6519	3135.3038	0.0000	1.0000
K2PG	37	-1532.6111	3139.2222	0.0000	1.0000
K2PIG	38	-1532.2910	3140.5821	0.0000	1.0000
K2PI	37	-1534.9184	3143.8368	0.0000	1.0000
GTR	43	-1551.1724	3188.3449	0.0000	1.0000
SYM	40	-1562.4314	3204.8627	0.0000	1.0000
HKY	39	-1564.3499	3206.6998	0.0000	1.0000
K2P	36	-1571.9252	3215.8503	0.0000	1.0000
F81G	39	-1571.1246	3220.2492	0.0000	1.0000
F81IG	40	-1570.8150	3221.6299	0.0000	1.0000
F81I	39	-1574.4133	3226.8265	0.0000	1.0000
JC69G	36	-1578.3459	3228.6917	0.0000	1.0000
JC69IG	37	-1578.0415	3230.0829	0.0000	1.0000
JC69I	36	-1581.8873	3235.7746	0.0000	1.0000
F81	38	-1605.9014	3287.8028	0.0000	1.0000
JC69	35	-1614.0939	3298.1879	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1532.6111	3288.7996	0.5749	0.5749
GTRG	44	-1512.5848	3291.0455	0.1870	0.7620
HKYG	40	-1525.5531	3292.8116	0.0773	0.8393
K2PI	37	-1534.9184	3293.4142	0.0572	0.8966
K2PIG	38	-1532.2910	3294.2021	0.0386	0.9351
SYMG	41	-1523.5951	3294.9381	0.0267	0.9619
GTRIG	45	-1512.0865	3296.0916	0.0150	0.9769
HKYI	40	-1527.6519	3297.0091	0.0095	0.9863
GTRI	44	-1516.1923	3298.2605	0.0051	0.9914
HKYIG	41	-1525.3057	3298.3593	0.0048	0.9962
SYMIG	42	-1523.0457	3299.8819	0.0023	0.9985
SYMI	41	-1526.4758	3300.6996	0.0015	1.0000
K2P	36	-1571.9252	3361.3851	0.0000	1.0000
GTR	43	-1551.1724	3362.1781	0.0000	1.0000
HKY	39	-1564.3499	3364.3624	0.0000	1.0000
SYM	40	-1562.4314	3366.5680	0.0000	1.0000
JC69G	36	-1578.3459	3374.2265	0.0000	1.0000
F81G	39	-1571.1246	3377.9118	0.0000	1.0000
JC69IG	37	-1578.0415	3379.6603	0.0000	1.0000
JC69I	36	-1581.8873	3381.3094	0.0000	1.0000
F81IG	40	-1570.8150	3383.3353	0.0000	1.0000
F81I	39	-1574.4133	3384.4892	0.0000	1.0000
JC69	35	-1614.0939	3439.6800	0.0000	1.0000
F81	38	-1605.9014	3441.4229	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_9078.phylip = 1 - 421;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9078.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/chr7_9078.phylip = 1 - 421;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9078.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/chr7_9078.phylip = 1 - 421;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9078.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

