
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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_2596.phylip" (19 taxa, 400 characters)

Minimum AIC  model: HKYG
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	-1080.7087	2250.5540	0.4257	0.4257
HKYI	40	-1080.9570	2251.0504	0.3322	0.7579
HKYIG	41	-1080.7259	2253.0719	0.1209	0.8788
HKY	39	-1084.1250	2254.9167	0.0481	0.9268
GTRG	44	-1078.2420	2255.6388	0.0335	0.9603
GTRI	44	-1078.5104	2256.1758	0.0256	0.9859
GTRIG	45	-1078.2418	2258.1785	0.0094	0.9953
GTR	43	-1081.6003	2259.8298	0.0041	0.9995
K2PG	37	-1092.4710	2266.7099	0.0001	0.9996
K2PI	37	-1092.6760	2267.1200	0.0001	0.9997
SYMG	41	-1087.7814	2267.1830	0.0001	0.9998
SYMI	41	-1088.0642	2267.7484	0.0001	0.9999
K2PIG	38	-1092.4765	2269.1635	0.0000	0.9999
SYMIG	42	-1087.7875	2269.6926	0.0000	1.0000
SYM	40	-1090.5419	2270.2203	0.0000	1.0000
K2P	36	-1095.6992	2270.7373	0.0000	1.0000
F81G	39	-1115.1001	2316.8669	0.0000	1.0000
F81I	39	-1115.4656	2317.5979	0.0000	1.0000
F81IG	40	-1115.1093	2319.3551	0.0000	1.0000
F81	38	-1118.6897	2321.5898	0.0000	1.0000
JC69G	36	-1127.0872	2333.5133	0.0000	1.0000
JC69I	36	-1127.4381	2334.2151	0.0000	1.0000
JC69IG	37	-1127.0870	2335.9419	0.0000	1.0000
JC69	35	-1130.2422	2337.4075	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1080.7087	2241.4175	0.3686	0.3686
HKYI	40	-1080.9570	2241.9139	0.2876	0.6562
HKYIG	41	-1080.7259	2243.4518	0.1333	0.7895
GTRG	44	-1078.2420	2244.4839	0.0796	0.8691
GTRI	44	-1078.5104	2245.0208	0.0608	0.9299
HKY	39	-1084.1250	2246.2500	0.0329	0.9628
GTRIG	45	-1078.2418	2246.4836	0.0293	0.9921
GTR	43	-1081.6003	2249.2006	0.0075	0.9996
SYMG	41	-1087.7814	2257.5629	0.0001	0.9997
SYMI	41	-1088.0642	2258.1283	0.0001	0.9998
K2PG	37	-1092.4710	2258.9420	0.0001	0.9999
K2PI	37	-1092.6760	2259.3520	0.0000	0.9999
SYMIG	42	-1087.7875	2259.5749	0.0000	1.0000
K2PIG	38	-1092.4765	2260.9530	0.0000	1.0000
SYM	40	-1090.5419	2261.0838	0.0000	1.0000
K2P	36	-1095.6992	2263.3984	0.0000	1.0000
F81G	39	-1115.1001	2308.2003	0.0000	1.0000
F81I	39	-1115.4656	2308.9312	0.0000	1.0000
F81IG	40	-1115.1093	2310.2186	0.0000	1.0000
F81	38	-1118.6897	2313.3793	0.0000	1.0000
JC69G	36	-1127.0872	2326.1745	0.0000	1.0000
JC69I	36	-1127.4381	2326.8763	0.0000	1.0000
JC69IG	37	-1127.0870	2328.1740	0.0000	1.0000
JC69	35	-1130.2422	2330.4844	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1080.7087	2401.0760	0.3771	0.3771
HKYI	40	-1080.9570	2401.5725	0.2942	0.6713
HKY	39	-1084.1250	2401.9172	0.2476	0.9189
K2PG	37	-1092.4710	2406.6262	0.0235	0.9424
K2PI	37	-1092.6760	2407.0362	0.0192	0.9615
K2P	36	-1095.6992	2407.0911	0.0186	0.9802
HKYIG	41	-1080.7259	2407.1018	0.0185	0.9987
K2PIG	38	-1092.4765	2412.6286	0.0012	0.9999
GTRG	44	-1078.2420	2420.1084	0.0000	0.9999
GTRI	44	-1078.5104	2420.6453	0.0000	0.9999
SYM	40	-1090.5419	2420.7424	0.0000	1.0000
GTR	43	-1081.6003	2420.8335	0.0000	1.0000
SYMG	41	-1087.7814	2421.2129	0.0000	1.0000
SYMI	41	-1088.0642	2421.7784	0.0000	1.0000
GTRIG	45	-1078.2418	2426.0995	0.0000	1.0000
SYMIG	42	-1087.7875	2427.2164	0.0000	1.0000
F81G	39	-1115.1001	2463.8674	0.0000	1.0000
F81I	39	-1115.4656	2464.5984	0.0000	1.0000
F81	38	-1118.6897	2465.0550	0.0000	1.0000
JC69G	36	-1127.0872	2469.8672	0.0000	1.0000
F81IG	40	-1115.1093	2469.8772	0.0000	1.0000
JC69	35	-1130.2422	2470.1857	0.0000	1.0000
JC69I	36	-1127.4381	2470.5690	0.0000	1.0000
JC69IG	37	-1127.0870	2475.8582	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2596.phylip = 1 - 400;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2596.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2596.phylip = 1 - 400;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2596.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/chr19_2596.phylip = 1 - 400;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr19_2596.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

