
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:02 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/chr8_3277.phylip" (19 taxa, 460 characters)

Minimum AIC  model: GTRI
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	-1138.7655	2365.3591	0.2900	0.2900
HKYI	40	-1138.7835	2365.3952	0.2848	0.5748
GTRI	44	-1134.6698	2366.8819	0.1354	0.7102
GTRG	44	-1134.6954	2366.9330	0.1320	0.8422
HKYIG	41	-1138.7682	2367.7756	0.0866	0.9288
GTRIG	45	-1134.6991	2369.3983	0.0385	0.9673
HKY	39	-1142.4407	2370.3100	0.0244	0.9917
GTR	43	-1138.6833	2372.4628	0.0083	1.0000
F81I	39	-1161.5296	2408.4877	0.0000	1.0000
F81G	39	-1161.5332	2408.4950	0.0000	1.0000
F81IG	40	-1161.5355	2410.8992	0.0000	1.0000
F81	38	-1164.8910	2412.8225	0.0000	1.0000
K2PG	37	-1170.4474	2421.5582	0.0000	1.0000
K2PI	37	-1170.4698	2421.6032	0.0000	1.0000
K2PIG	38	-1170.4504	2423.9412	0.0000	1.0000
K2P	36	-1173.7397	2425.7773	0.0000	1.0000
SYMI	41	-1168.7730	2427.7852	0.0000	1.0000
SYMG	41	-1168.7985	2427.8363	0.0000	1.0000
SYMIG	42	-1168.8010	2430.2638	0.0000	1.0000
SYM	40	-1171.8110	2431.4502	0.0000	1.0000
JC69I	36	-1189.7821	2457.8620	0.0000	1.0000
JC69G	36	-1189.8099	2457.9176	0.0000	1.0000
JC69IG	37	-1189.8119	2460.2873	0.0000	1.0000
JC69	35	-1192.8742	2461.6918	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1134.6698	2357.3397	0.2184	0.2184
GTRG	44	-1134.6954	2357.3908	0.2129	0.4313
HKYG	40	-1138.7655	2357.5309	0.1985	0.6298
HKYI	40	-1138.7835	2357.5671	0.1949	0.8247
GTRIG	45	-1134.6991	2359.3983	0.0780	0.9028
HKYIG	41	-1138.7682	2359.5364	0.0728	0.9756
HKY	39	-1142.4407	2362.8814	0.0137	0.9893
GTR	43	-1138.6833	2363.3666	0.0107	1.0000
F81I	39	-1161.5296	2401.0591	0.0000	1.0000
F81G	39	-1161.5332	2401.0664	0.0000	1.0000
F81IG	40	-1161.5355	2403.0710	0.0000	1.0000
F81	38	-1164.8910	2405.7821	0.0000	1.0000
K2PG	37	-1170.4474	2414.8947	0.0000	1.0000
K2PI	37	-1170.4698	2414.9397	0.0000	1.0000
K2PIG	38	-1170.4504	2416.9008	0.0000	1.0000
K2P	36	-1173.7397	2419.4794	0.0000	1.0000
SYMI	41	-1168.7730	2419.5459	0.0000	1.0000
SYMG	41	-1168.7985	2419.5971	0.0000	1.0000
SYMIG	42	-1168.8010	2421.6019	0.0000	1.0000
SYM	40	-1171.8110	2423.6220	0.0000	1.0000
JC69I	36	-1189.7821	2451.5641	0.0000	1.0000
JC69G	36	-1189.8099	2451.6197	0.0000	1.0000
JC69IG	37	-1189.8119	2453.6238	0.0000	1.0000
JC69	35	-1192.8742	2455.7484	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1138.7655	2522.7800	0.3887	0.3887
HKYI	40	-1138.7835	2522.8161	0.3817	0.7704
HKY	39	-1142.4407	2523.9993	0.2113	0.9817
HKYIG	41	-1138.7682	2528.9167	0.0181	0.9997
GTRI	44	-1134.6698	2539.1137	0.0001	0.9998
GTRG	44	-1134.6954	2539.1648	0.0001	1.0000
GTR	43	-1138.6833	2541.0094	0.0000	1.0000
GTRIG	45	-1134.6991	2545.3035	0.0000	1.0000
F81I	39	-1161.5296	2562.1770	0.0000	1.0000
F81G	39	-1161.5332	2562.1842	0.0000	1.0000
F81	38	-1164.8910	2562.7687	0.0000	1.0000
K2PG	37	-1170.4474	2567.7501	0.0000	1.0000
K2PI	37	-1170.4698	2567.7951	0.0000	1.0000
K2P	36	-1173.7397	2568.2036	0.0000	1.0000
F81IG	40	-1161.5355	2568.3201	0.0000	1.0000
K2PIG	38	-1170.4504	2573.8874	0.0000	1.0000
SYM	40	-1171.8110	2588.8711	0.0000	1.0000
SYMI	41	-1168.7730	2588.9262	0.0000	1.0000
SYMG	41	-1168.7985	2588.9774	0.0000	1.0000
SYMIG	42	-1168.8010	2595.1134	0.0000	1.0000
JC69I	36	-1189.7821	2600.2883	0.0000	1.0000
JC69	35	-1192.8742	2600.3413	0.0000	1.0000
JC69G	36	-1189.8099	2600.3439	0.0000	1.0000
JC69IG	37	-1189.8119	2606.4792	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3277.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr8_3277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3277.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/chr8_3277.phylip = 1 - 460;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3277.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

