
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:08 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_5739.phylip" (19 taxa, 432 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1298.7931	2698.3116	0.4839	0.4839
GTRG	44	-1300.0837	2698.4000	0.4630	0.9469
GTRI	44	-1302.6104	2703.4535	0.0370	0.9839
HKYIG	41	-1307.6869	2706.2045	0.0094	0.9933
HKYG	40	-1309.4266	2707.2420	0.0056	0.9989
HKYI	40	-1311.0097	2710.4081	0.0011	1.0000
SYMIG	42	-1316.6414	2726.5681	0.0000	1.0000
SYMG	41	-1318.1601	2727.1510	0.0000	1.0000
SYMI	41	-1320.1913	2731.2134	0.0000	1.0000
K2PIG	38	-1326.1952	2735.9323	0.0000	1.0000
K2PG	37	-1328.0566	2737.2503	0.0000	1.0000
K2PI	37	-1329.1845	2739.5061	0.0000	1.0000
F81IG	40	-1355.9005	2800.1897	0.0000	1.0000
F81G	39	-1357.2269	2800.4130	0.0000	1.0000
GTR	43	-1353.9627	2803.6779	0.0000	1.0000
F81I	39	-1359.1482	2804.2556	0.0000	1.0000
HKY	39	-1366.7701	2819.4995	0.0000	1.0000
JC69IG	37	-1373.6023	2828.3416	0.0000	1.0000
JC69G	36	-1376.1912	2831.1267	0.0000	1.0000
JC69I	36	-1377.8396	2834.4235	0.0000	1.0000
SYM	40	-1373.0919	2834.5725	0.0000	1.0000
K2P	36	-1387.8581	2854.4605	0.0000	1.0000
F81	38	-1413.4769	2910.4959	0.0000	1.0000
JC69	35	-1431.2573	2938.8783	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1298.7931	2687.5862	0.5496	0.5496
GTRG	44	-1300.0837	2688.1674	0.4110	0.9607
GTRI	44	-1302.6104	2693.2209	0.0328	0.9935
HKYIG	41	-1307.6869	2697.3738	0.0041	0.9976
HKYG	40	-1309.4266	2698.8532	0.0020	0.9996
HKYI	40	-1311.0097	2702.0193	0.0004	1.0000
SYMIG	42	-1316.6414	2717.2828	0.0000	1.0000
SYMG	41	-1318.1601	2718.3203	0.0000	1.0000
SYMI	41	-1320.1913	2722.3827	0.0000	1.0000
K2PIG	38	-1326.1952	2728.3903	0.0000	1.0000
K2PG	37	-1328.0566	2730.1132	0.0000	1.0000
K2PI	37	-1329.1845	2732.3691	0.0000	1.0000
F81IG	40	-1355.9005	2791.8010	0.0000	1.0000
F81G	39	-1357.2269	2792.4538	0.0000	1.0000
GTR	43	-1353.9627	2793.9254	0.0000	1.0000
F81I	39	-1359.1482	2796.2964	0.0000	1.0000
HKY	39	-1366.7701	2811.5403	0.0000	1.0000
JC69IG	37	-1373.6023	2821.2045	0.0000	1.0000
JC69G	36	-1376.1912	2824.3824	0.0000	1.0000
SYM	40	-1373.0919	2826.1838	0.0000	1.0000
JC69I	36	-1377.8396	2827.6792	0.0000	1.0000
K2P	36	-1387.8581	2847.7162	0.0000	1.0000
F81	38	-1413.4769	2902.9539	0.0000	1.0000
JC69	35	-1431.2573	2932.5147	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1309.4266	2861.5902	0.6426	0.6426
HKYIG	41	-1307.6869	2864.1792	0.1761	0.8186
HKYI	40	-1311.0097	2864.7563	0.1319	0.9506
GTRG	44	-1300.0837	2867.1782	0.0393	0.9899
GTRIG	45	-1298.7931	2870.6654	0.0069	0.9968
GTRI	44	-1302.6104	2872.2316	0.0031	0.9999
K2PG	37	-1328.0566	2880.6449	0.0000	1.0000
K2PI	37	-1329.1845	2882.9008	0.0000	1.0000
K2PIG	38	-1326.1952	2882.9905	0.0000	1.0000
SYMG	41	-1318.1601	2885.1257	0.0000	1.0000
SYMIG	42	-1316.6414	2888.1567	0.0000	1.0000
SYMI	41	-1320.1913	2889.1881	0.0000	1.0000
F81G	39	-1357.2269	2951.1224	0.0000	1.0000
F81IG	40	-1355.9005	2954.5380	0.0000	1.0000
F81I	39	-1359.1482	2954.9650	0.0000	1.0000
GTR	43	-1353.9627	2968.8677	0.0000	1.0000
HKY	39	-1366.7701	2970.2089	0.0000	1.0000
JC69G	36	-1376.1912	2970.8457	0.0000	1.0000
JC69IG	37	-1373.6023	2971.7363	0.0000	1.0000
JC69I	36	-1377.8396	2974.1425	0.0000	1.0000
SYM	40	-1373.0919	2988.9208	0.0000	1.0000
K2P	36	-1387.8581	2994.1795	0.0000	1.0000
F81	38	-1413.4769	3057.5541	0.0000	1.0000
JC69	35	-1431.2573	3074.9096	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5739.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5739.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5739.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5739.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr10_5739.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5739.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

