
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:57 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_10633.phylip" (19 taxa, 1019 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-2750.8529	5593.7715	0.6549	0.6549
GTRIG	45	-2750.7728	5595.8004	0.2375	0.8924
GTRG	44	-2752.8331	5597.7319	0.0904	0.9828
HKYI	40	-2759.2306	5601.8149	0.0117	0.9946
HKYIG	41	-2759.2634	5604.0518	0.0038	0.9984
HKYG	40	-2761.2212	5605.7962	0.0016	1.0000
GTR	43	-2771.1475	5632.1761	0.0000	1.0000
HKY	39	-2778.1923	5637.5715	0.0000	1.0000
F81I	39	-2786.2875	5653.7620	0.0000	1.0000
F81IG	40	-2786.3950	5656.1439	0.0000	1.0000
F81G	39	-2788.2710	5657.7289	0.0000	1.0000
F81	38	-2804.9857	5688.9959	0.0000	1.0000
SYMI	41	-2812.9195	5711.3640	0.0000	1.0000
SYMG	41	-2813.0335	5711.5921	0.0000	1.0000
SYMIG	42	-2813.0469	5713.7946	0.0000	1.0000
K2PI	37	-2818.6856	5714.2376	0.0000	1.0000
K2PG	37	-2818.8030	5714.4724	0.0000	1.0000
K2PIG	38	-2818.8621	5716.7486	0.0000	1.0000
SYM	40	-2834.1056	5751.5650	0.0000	1.0000
K2P	36	-2838.7861	5752.2851	0.0000	1.0000
JC69I	36	-2844.2994	5763.3116	0.0000	1.0000
JC69IG	37	-2844.4226	5765.7117	0.0000	1.0000
JC69G	36	-2846.2975	5767.3078	0.0000	1.0000
JC69	35	-2863.7355	5800.0345	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2750.8529	5589.7058	0.6429	0.6429
GTRIG	45	-2750.7728	5591.5456	0.2563	0.8992
GTRG	44	-2752.8331	5593.6662	0.0888	0.9880
HKYI	40	-2759.2306	5598.4611	0.0081	0.9960
HKYIG	41	-2759.2634	5600.5267	0.0029	0.9989
HKYG	40	-2761.2212	5602.4424	0.0011	1.0000
GTR	43	-2771.1475	5628.2951	0.0000	1.0000
HKY	39	-2778.1923	5634.3846	0.0000	1.0000
F81I	39	-2786.2875	5650.5751	0.0000	1.0000
F81IG	40	-2786.3950	5652.7901	0.0000	1.0000
F81G	39	-2788.2710	5654.5420	0.0000	1.0000
F81	38	-2804.9857	5685.9714	0.0000	1.0000
SYMI	41	-2812.9195	5707.8389	0.0000	1.0000
SYMG	41	-2813.0335	5708.0670	0.0000	1.0000
SYMIG	42	-2813.0469	5710.0938	0.0000	1.0000
K2PI	37	-2818.6856	5711.3712	0.0000	1.0000
K2PG	37	-2818.8030	5711.6059	0.0000	1.0000
K2PIG	38	-2818.8621	5713.7242	0.0000	1.0000
SYM	40	-2834.1056	5748.2112	0.0000	1.0000
K2P	36	-2838.7861	5749.5723	0.0000	1.0000
JC69I	36	-2844.2994	5760.5987	0.0000	1.0000
JC69IG	37	-2844.4226	5762.8453	0.0000	1.0000
JC69G	36	-2846.2975	5764.5950	0.0000	1.0000
JC69	35	-2863.7355	5797.4709	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2759.2306	5795.5242	0.8534	0.8534
HKYG	40	-2761.2212	5799.5055	0.1166	0.9699
HKYIG	41	-2759.2634	5802.5164	0.0259	0.9958
GTRI	44	-2750.8529	5806.4752	0.0036	0.9994
GTRG	44	-2752.8331	5810.4356	0.0005	0.9999
GTRIG	45	-2750.7728	5813.2415	0.0001	1.0000
HKY	39	-2778.1923	5826.5211	0.0000	1.0000
GTR	43	-2771.1475	5840.1379	0.0000	1.0000
F81I	39	-2786.2875	5842.7116	0.0000	1.0000
F81G	39	-2788.2710	5846.6785	0.0000	1.0000
F81IG	40	-2786.3950	5849.8532	0.0000	1.0000
F81	38	-2804.9857	5873.1814	0.0000	1.0000
K2PI	37	-2818.6856	5893.6545	0.0000	1.0000
K2PG	37	-2818.8030	5893.8893	0.0000	1.0000
K2PIG	38	-2818.8621	5900.9341	0.0000	1.0000
SYMI	41	-2812.9195	5909.8286	0.0000	1.0000
SYMG	41	-2813.0335	5910.0567	0.0000	1.0000
SYMIG	42	-2813.0469	5917.0100	0.0000	1.0000
K2P	36	-2838.7861	5926.9291	0.0000	1.0000
JC69I	36	-2844.2994	5937.9555	0.0000	1.0000
JC69G	36	-2846.2975	5941.9518	0.0000	1.0000
JC69IG	37	-2844.4226	5945.1286	0.0000	1.0000
SYM	40	-2834.1056	5945.2743	0.0000	1.0000
JC69	35	-2863.7355	5969.9011	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip = 1 - 1019;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip = 1 - 1019;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip = 1 - 1019;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10633.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

