
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/chr19_365.phylip" (19 taxa, 433 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-992.3898	2082.9859	0.4287	0.4287
GTRI	44	-992.5921	2083.3903	0.3502	0.7790
GTRIG	45	-992.2075	2085.1126	0.1480	0.9270
HKYG	40	-999.9381	2088.2436	0.0309	0.9579
HKYI	40	-1000.0391	2088.4456	0.0280	0.9859
HKYIG	41	-999.5046	2089.8174	0.0141	1.0000
GTR	43	-1004.6554	2105.0384	0.0000	1.0000
HKY	39	-1012.7267	2111.3924	0.0000	1.0000
SYMG	41	-1012.0721	2114.9523	0.0000	1.0000
SYMI	41	-1012.3604	2115.5290	0.0000	1.0000
K2PG	37	-1017.6308	2116.3806	0.0000	1.0000
K2PI	37	-1017.6902	2116.4994	0.0000	1.0000
SYMIG	42	-1011.7751	2116.8117	0.0000	1.0000
K2PIG	38	-1017.2039	2117.9306	0.0000	1.0000
SYM	40	-1022.6454	2133.6581	0.0000	1.0000
F81G	39	-1025.6846	2137.3081	0.0000	1.0000
F81I	39	-1025.8211	2137.5811	0.0000	1.0000
K2P	36	-1029.6449	2138.0170	0.0000	1.0000
F81IG	40	-1025.3482	2139.0638	0.0000	1.0000
F81	38	-1035.7822	2155.0873	0.0000	1.0000
JC69G	36	-1041.2745	2161.2763	0.0000	1.0000
JC69I	36	-1041.4296	2161.5865	0.0000	1.0000
JC69IG	37	-1041.0027	2163.1244	0.0000	1.0000
JC69	35	-1050.7814	2177.9104	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-992.3898	2072.7797	0.4293	0.4293
GTRI	44	-992.5921	2073.1841	0.3507	0.7800
GTRIG	45	-992.2075	2074.4149	0.1895	0.9695
HKYG	40	-999.9381	2079.8762	0.0124	0.9818
HKYI	40	-1000.0391	2080.0783	0.0112	0.9930
HKYIG	41	-999.5046	2081.0093	0.0070	1.0000
GTR	43	-1004.6554	2095.3109	0.0000	1.0000
HKY	39	-1012.7267	2103.4535	0.0000	1.0000
SYMG	41	-1012.0721	2106.1441	0.0000	1.0000
SYMI	41	-1012.3604	2106.7208	0.0000	1.0000
SYMIG	42	-1011.7751	2107.5502	0.0000	1.0000
K2PG	37	-1017.6308	2109.2616	0.0000	1.0000
K2PI	37	-1017.6902	2109.3805	0.0000	1.0000
K2PIG	38	-1017.2039	2110.4078	0.0000	1.0000
SYM	40	-1022.6454	2125.2907	0.0000	1.0000
F81G	39	-1025.6846	2129.3691	0.0000	1.0000
F81I	39	-1025.8211	2129.6422	0.0000	1.0000
F81IG	40	-1025.3482	2130.6964	0.0000	1.0000
K2P	36	-1029.6449	2131.2898	0.0000	1.0000
F81	38	-1035.7822	2147.5645	0.0000	1.0000
JC69G	36	-1041.2745	2154.5490	0.0000	1.0000
JC69I	36	-1041.4296	2154.8592	0.0000	1.0000
JC69IG	37	-1041.0027	2156.0054	0.0000	1.0000
JC69	35	-1050.7814	2171.5628	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-999.9381	2242.7057	0.5006	0.5006
HKYI	40	-1000.0391	2242.9078	0.4525	0.9532
HKYIG	41	-999.5046	2247.9095	0.0371	0.9903
GTRG	44	-992.3898	2251.8921	0.0051	0.9954
GTRI	44	-992.5921	2252.2966	0.0041	0.9995
GTRIG	45	-992.2075	2257.5981	0.0003	0.9998
K2PG	37	-1017.6308	2259.8789	0.0001	0.9999
K2PI	37	-1017.6902	2259.9978	0.0001	1.0000
HKY	39	-1012.7267	2262.2123	0.0000	1.0000
K2PIG	38	-1017.2039	2265.0958	0.0000	1.0000
GTR	43	-1004.6554	2270.3526	0.0000	1.0000
SYMG	41	-1012.0721	2273.0444	0.0000	1.0000
SYMI	41	-1012.3604	2273.6211	0.0000	1.0000
K2P	36	-1029.6449	2277.8363	0.0000	1.0000
SYMIG	42	-1011.7751	2278.5211	0.0000	1.0000
SYM	40	-1022.6454	2288.1202	0.0000	1.0000
F81G	39	-1025.6846	2288.1279	0.0000	1.0000
F81I	39	-1025.8211	2288.4010	0.0000	1.0000
F81IG	40	-1025.3482	2293.5259	0.0000	1.0000
JC69G	36	-1041.2745	2301.0956	0.0000	1.0000
JC69I	36	-1041.4296	2301.4058	0.0000	1.0000
F81	38	-1035.7822	2302.2525	0.0000	1.0000
JC69IG	37	-1041.0027	2306.6227	0.0000	1.0000
JC69	35	-1050.7814	2314.0386	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/chr19_365.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_365.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/chr19_365.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_365.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_365.phylip = 1 - 433;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_365.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

