
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:19 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_11018.phylip" (19 taxa, 924 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: K2PG


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
SYMG	41	-2749.6270	5585.1587	0.4371	0.4371
SYMI	41	-2750.3665	5586.6377	0.2087	0.6458
SYMIG	42	-2749.3688	5586.8374	0.1888	0.8346
GTRG	44	-2748.1887	5588.8824	0.0679	0.9025
GTRI	44	-2748.8367	5590.1785	0.0355	0.9381
GTRIG	45	-2747.9745	5590.6642	0.0279	0.9659
K2PG	37	-2757.8359	5592.8456	0.0094	0.9753
HKYG	40	-2754.7436	5593.2017	0.0078	0.9831
K2PI	37	-2758.4206	5594.0150	0.0052	0.9884
HKYI	40	-2755.2350	5594.1847	0.0048	0.9932
K2PIG	38	-2757.6325	5594.6141	0.0039	0.9970
HKYIG	41	-2754.6152	5595.1353	0.0030	1.0000
SYM	40	-2810.1139	5703.9425	0.0000	1.0000
GTR	43	-2808.7231	5707.7462	0.0000	1.0000
K2P	36	-2819.4622	5713.9278	0.0000	1.0000
HKY	39	-2817.3204	5716.1702	0.0000	1.0000
JC69G	36	-2834.1696	5743.3425	0.0000	1.0000
JC69I	36	-2834.8484	5744.7002	0.0000	1.0000
F81G	39	-2831.7647	5745.0588	0.0000	1.0000
JC69IG	37	-2833.9717	5745.1172	0.0000	1.0000
F81I	39	-2832.4327	5746.3948	0.0000	1.0000
F81IG	40	-2831.5669	5746.8483	0.0000	1.0000
JC69	35	-2890.9027	5854.6433	0.0000	1.0000
F81	38	-2888.6298	5856.6088	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-2749.6270	5581.2539	0.4112	0.4112
SYMI	41	-2750.3665	5582.7330	0.1963	0.6075
SYMIG	42	-2749.3688	5582.7375	0.1959	0.8034
GTRG	44	-2748.1887	5584.3773	0.0863	0.8897
GTRI	44	-2748.8367	5585.6734	0.0451	0.9348
GTRIG	45	-2747.9745	5585.9490	0.0393	0.9741
HKYG	40	-2754.7436	5589.4871	0.0067	0.9808
K2PG	37	-2757.8359	5589.6718	0.0061	0.9869
HKYI	40	-2755.2350	5590.4701	0.0041	0.9910
K2PI	37	-2758.4206	5590.8412	0.0034	0.9944
HKYIG	41	-2754.6152	5591.2305	0.0028	0.9972
K2PIG	38	-2757.6325	5591.2650	0.0028	1.0000
SYM	40	-2810.1139	5700.2279	0.0000	1.0000
GTR	43	-2808.7231	5703.4462	0.0000	1.0000
K2P	36	-2819.4622	5710.9244	0.0000	1.0000
HKY	39	-2817.3204	5712.6408	0.0000	1.0000
JC69G	36	-2834.1696	5740.3391	0.0000	1.0000
F81G	39	-2831.7647	5741.5294	0.0000	1.0000
JC69I	36	-2834.8484	5741.6969	0.0000	1.0000
JC69IG	37	-2833.9717	5741.9433	0.0000	1.0000
F81I	39	-2832.4327	5742.8654	0.0000	1.0000
F81IG	40	-2831.5669	5743.1337	0.0000	1.0000
JC69	35	-2890.9027	5851.8054	0.0000	1.0000
F81	38	-2888.6298	5853.2596	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2757.8359	5768.3342	0.6229	0.6229
K2PI	37	-2758.4206	5769.5035	0.3471	0.9700
K2PIG	38	-2757.6325	5774.7560	0.0251	0.9951
SYMG	41	-2749.6270	5779.2311	0.0027	0.9978
SYMI	41	-2750.3665	5780.7102	0.0013	0.9991
HKYG	40	-2754.7436	5782.6356	0.0005	0.9996
HKYI	40	-2755.2350	5783.6185	0.0003	0.9999
SYMIG	42	-2749.3688	5785.5434	0.0001	1.0000
HKYIG	41	-2754.6152	5789.2077	0.0000	1.0000
GTRG	44	-2748.1887	5796.8406	0.0000	1.0000
GTRI	44	-2748.8367	5798.1368	0.0000	1.0000
GTRIG	45	-2747.9745	5803.2410	0.0000	1.0000
K2P	36	-2819.4622	5884.7581	0.0000	1.0000
SYM	40	-2810.1139	5893.3763	0.0000	1.0000
HKY	39	-2817.3204	5900.9606	0.0000	1.0000
GTR	43	-2808.7231	5911.0808	0.0000	1.0000
JC69G	36	-2834.1696	5914.1728	0.0000	1.0000
JC69I	36	-2834.8484	5915.5305	0.0000	1.0000
JC69IG	37	-2833.9717	5920.6057	0.0000	1.0000
F81G	39	-2831.7647	5929.8492	0.0000	1.0000
F81I	39	-2832.4327	5931.1851	0.0000	1.0000
F81IG	40	-2831.5669	5936.2822	0.0000	1.0000
JC69	35	-2890.9027	6020.8104	0.0000	1.0000
F81	38	-2888.6298	6036.7507	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.phylip = 1 - 924;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11018.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


-------------------------------------------------------------
End of Output

