
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:00 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/chr5_10841.phylip" (19 taxa, 382 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-1028.1690	2145.9567	0.3614	0.3614
HKYG	40	-1028.2583	2146.1353	0.3306	0.6920
HKYIG	41	-1027.4634	2147.0561	0.2086	0.9006
GTRG	44	-1024.9947	2149.7401	0.0545	0.9551
GTRI	44	-1025.6735	2151.0978	0.0276	0.9827
GTRIG	45	-1024.8944	2152.1102	0.0167	0.9994
HKY	39	-1035.8374	2158.7975	0.0006	1.0000
GTR	43	-1034.0542	2165.3036	0.0000	1.0000
F81G	39	-1045.7464	2178.6155	0.0000	1.0000
F81I	39	-1046.2357	2179.5942	0.0000	1.0000
F81IG	40	-1045.4655	2180.5498	0.0000	1.0000
F81	38	-1052.2043	2189.0499	0.0000	1.0000
K2PG	37	-1055.1026	2192.3796	0.0000	1.0000
SYMG	41	-1050.2031	2192.5355	0.0000	1.0000
K2PI	37	-1056.3733	2194.9210	0.0000	1.0000
SYMI	41	-1051.4336	2194.9967	0.0000	1.0000
SYMIG	42	-1050.3672	2195.3892	0.0000	1.0000
K2PIG	38	-1055.5186	2195.6786	0.0000	1.0000
K2P	36	-1062.0350	2203.7917	0.0000	1.0000
SYM	40	-1057.6674	2204.9536	0.0000	1.0000
JC69G	36	-1069.7896	2219.3009	0.0000	1.0000
JC69I	36	-1071.5274	2222.7766	0.0000	1.0000
JC69IG	37	-1070.6848	2223.5441	0.0000	1.0000
JC69	35	-1075.9632	2229.2096	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1028.1690	2136.3380	0.2858	0.2858
HKYG	40	-1028.2583	2136.5165	0.2614	0.5472
HKYIG	41	-1027.4634	2136.9267	0.2129	0.7601
GTRG	44	-1024.9947	2137.9894	0.1252	0.8852
GTRI	44	-1025.6735	2139.3471	0.0635	0.9487
GTRIG	45	-1024.8944	2139.7888	0.0509	0.9996
HKY	39	-1035.8374	2149.6747	0.0004	1.0000
GTR	43	-1034.0542	2154.1083	0.0000	1.0000
F81G	39	-1045.7464	2169.4927	0.0000	1.0000
F81I	39	-1046.2357	2170.4714	0.0000	1.0000
F81IG	40	-1045.4655	2170.9310	0.0000	1.0000
F81	38	-1052.2043	2180.4085	0.0000	1.0000
SYMG	41	-1050.2031	2182.4061	0.0000	1.0000
K2PG	37	-1055.1026	2184.2052	0.0000	1.0000
SYMIG	42	-1050.3672	2184.7343	0.0000	1.0000
SYMI	41	-1051.4336	2184.8673	0.0000	1.0000
K2PI	37	-1056.3733	2186.7465	0.0000	1.0000
K2PIG	38	-1055.5186	2187.0372	0.0000	1.0000
SYM	40	-1057.6674	2195.3348	0.0000	1.0000
K2P	36	-1062.0350	2196.0700	0.0000	1.0000
JC69G	36	-1069.7896	2211.5792	0.0000	1.0000
JC69I	36	-1071.5274	2215.0548	0.0000	1.0000
JC69IG	37	-1070.6848	2215.3696	0.0000	1.0000
JC69	35	-1075.9632	2221.9264	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1028.1690	2294.1548	0.4932	0.4932
HKYG	40	-1028.2583	2294.3334	0.4511	0.9443
HKYIG	41	-1027.4634	2298.6890	0.0511	0.9954
HKY	39	-1035.8374	2303.5461	0.0045	0.9999
GTRG	44	-1024.9947	2311.5879	0.0001	1.0000
GTRI	44	-1025.6735	2312.9456	0.0000	1.0000
GTRIG	45	-1024.8944	2317.3327	0.0000	1.0000
F81G	39	-1045.7464	2323.3641	0.0000	1.0000
GTR	43	-1034.0542	2323.7614	0.0000	1.0000
F81I	39	-1046.2357	2324.3428	0.0000	1.0000
F81IG	40	-1045.4655	2328.7478	0.0000	1.0000
K2PG	37	-1055.1026	2330.1857	0.0000	1.0000
F81	38	-1052.2043	2330.3345	0.0000	1.0000
K2PI	37	-1056.3733	2332.7271	0.0000	1.0000
K2PIG	38	-1055.5186	2336.9632	0.0000	1.0000
K2P	36	-1062.0350	2338.1051	0.0000	1.0000
SYMG	41	-1050.2031	2344.1684	0.0000	1.0000
SYMI	41	-1051.4336	2346.6295	0.0000	1.0000
SYMIG	42	-1050.3672	2350.4420	0.0000	1.0000
SYM	40	-1057.6674	2353.1516	0.0000	1.0000
JC69G	36	-1069.7896	2353.6143	0.0000	1.0000
JC69I	36	-1071.5274	2357.0900	0.0000	1.0000
JC69	35	-1075.9632	2360.0161	0.0000	1.0000
JC69IG	37	-1070.6848	2361.3502	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10841.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

