
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:11 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/chr1_5411.phylip" (19 taxa, 299 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	-1010.5595	2113.8322	0.2738	0.2738
HKYI	40	-1010.7696	2114.2524	0.2219	0.4957
GTRG	44	-1005.4245	2114.4395	0.2021	0.6978
GTRI	44	-1005.7366	2115.0637	0.1479	0.8457
HKYIG	41	-1010.3251	2116.0510	0.0903	0.9359
GTRIG	45	-1005.1871	2116.7379	0.0640	1.0000
GTR	43	-1016.7157	2134.2705	0.0000	1.0000
HKY	39	-1022.6643	2135.3749	0.0000	1.0000
K2PG	37	-1050.6716	2186.1171	0.0000	1.0000
K2PI	37	-1051.5838	2187.9416	0.0000	1.0000
K2PIG	38	-1050.5874	2188.5749	0.0000	1.0000
SYMG	41	-1048.7147	2192.8301	0.0000	1.0000
SYMI	41	-1049.8017	2195.0041	0.0000	1.0000
SYMIG	42	-1048.6797	2195.4688	0.0000	1.0000
K2P	36	-1066.3034	2214.7748	0.0000	1.0000
SYM	40	-1063.1007	2218.9146	0.0000	1.0000
F81G	39	-1066.5740	2223.1943	0.0000	1.0000
F81I	39	-1066.9329	2223.9121	0.0000	1.0000
F81IG	40	-1066.5052	2225.7235	0.0000	1.0000
F81	38	-1078.8992	2245.1985	0.0000	1.0000
JC69G	36	-1096.7974	2275.7628	0.0000	1.0000
JC69I	36	-1097.4711	2277.1102	0.0000	1.0000
JC69IG	37	-1096.7477	2278.2693	0.0000	1.0000
JC69	35	-1110.9686	2301.5189	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1005.4245	2098.8489	0.3413	0.3413
GTRI	44	-1005.7366	2099.4732	0.2498	0.5911
GTRIG	45	-1005.1871	2100.3743	0.1592	0.7503
HKYG	40	-1010.5595	2101.1190	0.1097	0.8601
HKYI	40	-1010.7696	2101.5392	0.0889	0.9490
HKYIG	41	-1010.3251	2102.6502	0.0510	1.0000
GTR	43	-1016.7157	2119.4313	0.0000	1.0000
HKY	39	-1022.6643	2123.3285	0.0000	1.0000
K2PG	37	-1050.6716	2175.3432	0.0000	1.0000
K2PI	37	-1051.5838	2177.1677	0.0000	1.0000
K2PIG	38	-1050.5874	2177.1749	0.0000	1.0000
SYMG	41	-1048.7147	2179.4293	0.0000	1.0000
SYMIG	42	-1048.6797	2181.3594	0.0000	1.0000
SYMI	41	-1049.8017	2181.6034	0.0000	1.0000
K2P	36	-1066.3034	2204.6068	0.0000	1.0000
SYM	40	-1063.1007	2206.2014	0.0000	1.0000
F81G	39	-1066.5740	2211.1479	0.0000	1.0000
F81I	39	-1066.9329	2211.8658	0.0000	1.0000
F81IG	40	-1066.5052	2213.0104	0.0000	1.0000
F81	38	-1078.8992	2233.7985	0.0000	1.0000
JC69G	36	-1096.7974	2265.5949	0.0000	1.0000
JC69I	36	-1097.4711	2266.9422	0.0000	1.0000
JC69IG	37	-1096.7477	2267.4953	0.0000	1.0000
JC69	35	-1110.9686	2291.9372	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1010.5595	2249.1367	0.5299	0.5299
HKYI	40	-1010.7696	2249.5569	0.4295	0.9594
HKYIG	41	-1010.3251	2254.3684	0.0387	0.9981
GTRG	44	-1005.4245	2261.6684	0.0010	0.9991
GTRI	44	-1005.7366	2262.2927	0.0007	0.9999
GTRIG	45	-1005.1871	2266.8943	0.0001	0.9999
HKY	39	-1022.6643	2267.6458	0.0001	1.0000
GTR	43	-1016.7157	2278.5504	0.0000	1.0000
K2PG	37	-1050.6716	2312.2596	0.0000	1.0000
K2PI	37	-1051.5838	2314.0841	0.0000	1.0000
K2PIG	38	-1050.5874	2317.7917	0.0000	1.0000
SYMG	41	-1048.7147	2331.1475	0.0000	1.0000
SYMI	41	-1049.8017	2333.3215	0.0000	1.0000
SYMIG	42	-1048.6797	2336.7781	0.0000	1.0000
K2P	36	-1066.3034	2337.8228	0.0000	1.0000
SYM	40	-1063.1007	2354.2191	0.0000	1.0000
F81G	39	-1066.5740	2355.4652	0.0000	1.0000
F81I	39	-1066.9329	2356.1831	0.0000	1.0000
F81IG	40	-1066.5052	2361.0281	0.0000	1.0000
F81	38	-1078.8992	2374.4154	0.0000	1.0000
JC69G	36	-1096.7974	2398.8108	0.0000	1.0000
JC69I	36	-1097.4711	2400.1582	0.0000	1.0000
JC69IG	37	-1096.7477	2404.4118	0.0000	1.0000
JC69	35	-1110.9686	2421.4527	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/chr1_5411.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5411.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/chr1_5411.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5411.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/chr1_5411.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5411.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

