
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:36 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_10180.phylip" (19 taxa, 612 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: SYMG


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	-3148.9344	6392.8529	0.7049	0.7049
GTRIG	45	-3148.9033	6395.1211	0.2268	0.9317
SYMG	41	-3155.0802	6398.2025	0.0486	0.9803
SYMIG	42	-3155.0876	6400.5232	0.0152	0.9955
HKYG	40	-3158.9003	6403.5449	0.0034	0.9989
HKYIG	41	-3158.8620	6405.7660	0.0011	1.0000
HKYI	40	-3164.4363	6414.6169	0.0000	1.0000
K2PG	37	-3168.0582	6415.0153	0.0000	1.0000
GTRI	44	-3160.5989	6416.1819	0.0000	1.0000
SYMI	41	-3164.4518	6416.9456	0.0000	1.0000
K2PIG	38	-3168.0732	6417.3192	0.0000	1.0000
K2PI	37	-3173.8067	6426.5124	0.0000	1.0000
HKY	39	-3215.1088	6513.6721	0.0000	1.0000
GTR	43	-3212.6061	6517.8743	0.0000	1.0000
K2P	36	-3224.0505	6524.7340	0.0000	1.0000
SYM	40	-3219.6447	6525.0336	0.0000	1.0000
F81G	39	-3246.7514	6576.9573	0.0000	1.0000
F81IG	40	-3246.1862	6578.1168	0.0000	1.0000
JC69G	36	-3254.0483	6584.7296	0.0000	1.0000
JC69IG	37	-3253.0575	6585.0139	0.0000	1.0000
F81I	39	-3252.4365	6588.3276	0.0000	1.0000
JC69I	36	-3259.8522	6596.3375	0.0000	1.0000
F81	38	-3298.5801	6678.3331	0.0000	1.0000
JC69	35	-3305.8662	6686.1074	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3148.9344	6385.8688	0.6936	0.6936
GTRIG	45	-3148.9033	6387.8066	0.2632	0.9568
SYMG	41	-3155.0802	6392.1604	0.0298	0.9866
SYMIG	42	-3155.0876	6394.1752	0.0109	0.9975
HKYG	40	-3158.9003	6397.8006	0.0018	0.9993
HKYIG	41	-3158.8620	6399.7239	0.0007	1.0000
HKYI	40	-3164.4363	6408.8726	0.0000	1.0000
GTRI	44	-3160.5989	6409.1978	0.0000	1.0000
K2PG	37	-3168.0582	6410.1164	0.0000	1.0000
SYMI	41	-3164.4518	6410.9035	0.0000	1.0000
K2PIG	38	-3168.0732	6412.1465	0.0000	1.0000
K2PI	37	-3173.8067	6421.6135	0.0000	1.0000
HKY	39	-3215.1088	6508.2176	0.0000	1.0000
GTR	43	-3212.6061	6511.2123	0.0000	1.0000
SYM	40	-3219.6447	6519.2893	0.0000	1.0000
K2P	36	-3224.0505	6520.1010	0.0000	1.0000
F81G	39	-3246.7514	6571.5027	0.0000	1.0000
F81IG	40	-3246.1862	6572.3725	0.0000	1.0000
JC69G	36	-3254.0483	6580.0965	0.0000	1.0000
JC69IG	37	-3253.0575	6580.1150	0.0000	1.0000
F81I	39	-3252.4365	6582.8730	0.0000	1.0000
JC69I	36	-3259.8522	6591.7045	0.0000	1.0000
F81	38	-3298.5801	6673.1603	0.0000	1.0000
JC69	35	-3305.8662	6681.7324	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-3155.0802	6573.2464	0.3933	0.3933
K2PG	37	-3168.0582	6573.5355	0.3404	0.7338
HKYG	40	-3158.9003	6574.4699	0.2134	0.9471
SYMIG	42	-3155.0876	6579.6780	0.0158	0.9629
K2PIG	38	-3168.0732	6579.9823	0.0136	0.9764
GTRG	44	-3148.9344	6580.2050	0.0121	0.9886
HKYIG	41	-3158.8620	6580.8099	0.0090	0.9975
K2PI	37	-3173.8067	6585.0326	0.0011	0.9986
HKYI	40	-3164.4363	6585.5419	0.0008	0.9995
GTRIG	45	-3148.9033	6586.5595	0.0005	1.0000
SYMI	41	-3164.4518	6591.9896	0.0000	1.0000
GTRI	44	-3160.5989	6603.5340	0.0000	1.0000
K2P	36	-3224.0505	6679.1033	0.0000	1.0000
HKY	39	-3215.1088	6680.4701	0.0000	1.0000
SYM	40	-3219.6447	6695.9586	0.0000	1.0000
GTR	43	-3212.6061	6701.1318	0.0000	1.0000
JC69G	36	-3254.0483	6739.0989	0.0000	1.0000
JC69IG	37	-3253.0575	6743.5341	0.0000	1.0000
F81G	39	-3246.7514	6743.7553	0.0000	1.0000
F81IG	40	-3246.1862	6749.0418	0.0000	1.0000
JC69I	36	-3259.8522	6750.7069	0.0000	1.0000
F81I	39	-3252.4365	6755.1256	0.0000	1.0000
JC69	35	-3305.8662	6836.3181	0.0000	1.0000
F81	38	-3298.5801	6840.9961	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/chr5_10180.phylip = 1 - 612;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10180.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/chr5_10180.phylip = 1 - 612;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10180.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 (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10180.phylip = 1 - 612;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10180.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=Fixed(Equal);
END;


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End of Output

