
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:31 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/chrZ_6578.phylip" (19 taxa, 290 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-997.7055	2088.5837	0.3952	0.3952
HKYI	40	-998.3445	2089.8616	0.2086	0.6038
GTRG	44	-993.1768	2090.5168	0.1503	0.7542
HKYIG	41	-997.7134	2091.3139	0.1009	0.8551
GTRI	44	-993.7659	2091.6951	0.0834	0.9385
GTRIG	45	-993.2734	2093.5140	0.0336	0.9721
HKY	39	-1001.9249	2094.3299	0.0223	0.9944
GTR	43	-997.8957	2097.1735	0.0054	0.9998
K2PG	37	-1009.7990	2104.7568	0.0001	0.9999
K2PI	37	-1010.9118	2106.9823	0.0000	1.0000
K2PIG	38	-1010.3337	2108.4761	0.0000	1.0000
K2P	36	-1014.0663	2110.6622	0.0000	1.0000
SYMG	41	-1008.0912	2112.0696	0.0000	1.0000
SYMI	41	-1009.1031	2114.0934	0.0000	1.0000
SYMIG	42	-1008.5440	2115.7114	0.0000	1.0000
SYM	40	-1012.6141	2118.4009	0.0000	1.0000
F81G	39	-1022.5411	2135.5622	0.0000	1.0000
F81I	39	-1022.8820	2136.2440	0.0000	1.0000
F81IG	40	-1022.6323	2138.4372	0.0000	1.0000
F81	38	-1025.9101	2139.6290	0.0000	1.0000
JC69G	36	-1032.2063	2146.9423	0.0000	1.0000
JC69I	36	-1033.0805	2148.6906	0.0000	1.0000
JC69IG	37	-1032.8097	2150.7781	0.0000	1.0000
JC69	35	-1035.7135	2151.3484	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-993.1768	2074.3536	0.3276	0.3276
HKYG	40	-997.7055	2075.4110	0.1931	0.5207
GTRI	44	-993.7659	2075.5319	0.1818	0.7025
GTRIG	45	-993.2734	2076.5468	0.1094	0.8119
HKYI	40	-998.3445	2076.6889	0.1019	0.9138
HKYIG	41	-997.7134	2077.4268	0.0705	0.9843
GTR	43	-997.8957	2081.7914	0.0079	0.9922
HKY	39	-1001.9249	2081.8499	0.0077	1.0000
K2PG	37	-1009.7990	2093.5980	0.0000	1.0000
K2PI	37	-1010.9118	2095.8236	0.0000	1.0000
K2PIG	38	-1010.3337	2096.6674	0.0000	1.0000
SYMG	41	-1008.0912	2098.1825	0.0000	1.0000
K2P	36	-1014.0663	2100.1325	0.0000	1.0000
SYMI	41	-1009.1031	2100.2063	0.0000	1.0000
SYMIG	42	-1008.5440	2101.0880	0.0000	1.0000
SYM	40	-1012.6141	2105.2282	0.0000	1.0000
F81G	39	-1022.5411	2123.0822	0.0000	1.0000
F81I	39	-1022.8820	2123.7640	0.0000	1.0000
F81IG	40	-1022.6323	2125.2645	0.0000	1.0000
F81	38	-1025.9101	2127.8202	0.0000	1.0000
JC69G	36	-1032.2063	2136.4127	0.0000	1.0000
JC69I	36	-1033.0805	2138.1610	0.0000	1.0000
JC69IG	37	-1032.8097	2139.6194	0.0000	1.0000
JC69	35	-1035.7135	2141.4271	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-997.7055	2222.2063	0.5311	0.5311
HKYI	40	-998.3445	2223.4842	0.2804	0.8115
HKY	39	-1001.9249	2224.9752	0.1330	0.9445
HKYIG	41	-997.7134	2227.8919	0.0309	0.9755
K2PG	37	-1009.7990	2229.3836	0.0147	0.9901
K2PI	37	-1010.9118	2231.6092	0.0048	0.9950
K2P	36	-1014.0663	2232.2482	0.0035	0.9985
GTRG	44	-993.1768	2235.8283	0.0006	0.9990
K2PIG	38	-1010.3337	2236.1228	0.0005	0.9996
GTRI	44	-993.7659	2237.0066	0.0003	0.9999
GTR	43	-997.8957	2239.5962	0.0001	1.0000
GTRIG	45	-993.2734	2241.6914	0.0000	1.0000
SYMG	41	-1008.0912	2248.6476	0.0000	1.0000
SYMI	41	-1009.1031	2250.6714	0.0000	1.0000
SYM	40	-1012.6141	2252.0235	0.0000	1.0000
SYMIG	42	-1008.5440	2255.2230	0.0000	1.0000
F81G	39	-1022.5411	2266.2076	0.0000	1.0000
F81I	39	-1022.8820	2266.8893	0.0000	1.0000
F81	38	-1025.9101	2267.2757	0.0000	1.0000
JC69G	36	-1032.2063	2268.5284	0.0000	1.0000
JC69	35	-1035.7135	2269.8729	0.0000	1.0000
JC69I	36	-1033.0805	2270.2767	0.0000	1.0000
F81IG	40	-1022.6323	2272.0598	0.0000	1.0000
JC69IG	37	-1032.8097	2275.4050	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/chrZ_6578.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6578.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6578.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6578.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;


[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/chrZ_6578.phylip = 1 - 290;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6578.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

