
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:34 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_15412.phylip" (19 taxa, 1133 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3566.3025	7224.2447	0.6629	0.6629
GTRIG	45	-3566.0154	7225.8394	0.2986	0.9615
GTRI	44	-3569.1768	7229.9934	0.0374	0.9990
HKYG	40	-3577.5860	7238.1756	0.0006	0.9996
HKYIG	41	-3577.1366	7239.4300	0.0003	0.9999
SYMG	41	-3579.2885	7243.7337	0.0000	1.0000
HKYI	40	-3580.8618	7244.7273	0.0000	1.0000
SYMIG	42	-3578.9362	7245.1862	0.0000	1.0000
SYMI	41	-3582.4653	7250.0874	0.0000	1.0000
K2PG	37	-3587.0253	7250.6187	0.0000	1.0000
K2PIG	38	-3586.4779	7251.6651	0.0000	1.0000
K2PI	37	-3590.3989	7257.3657	0.0000	1.0000
GTR	43	-3621.2011	7331.8768	0.0000	1.0000
HKY	39	-3631.5932	7344.0409	0.0000	1.0000
SYM	40	-3634.5814	7352.1665	0.0000	1.0000
K2P	36	-3642.1574	7358.7455	0.0000	1.0000
F81G	39	-3682.8400	7446.5345	0.0000	1.0000
F81IG	40	-3682.4305	7447.8646	0.0000	1.0000
F81I	39	-3686.0231	7452.9007	0.0000	1.0000
JC69G	36	-3690.3922	7455.2150	0.0000	1.0000
JC69IG	37	-3689.9546	7456.4772	0.0000	1.0000
JC69I	36	-3693.6534	7461.7374	0.0000	1.0000
F81	38	-3735.0737	7548.8567	0.0000	1.0000
JC69	35	-3743.2280	7558.7533	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3566.3025	7220.6050	0.6460	0.6460
GTRIG	45	-3566.0154	7222.0308	0.3167	0.9628
GTRI	44	-3569.1768	7226.3537	0.0365	0.9992
HKYG	40	-3577.5860	7235.1719	0.0004	0.9997
HKYIG	41	-3577.1366	7236.2732	0.0003	0.9999
SYMG	41	-3579.2885	7240.5769	0.0000	1.0000
HKYI	40	-3580.8618	7241.7237	0.0000	1.0000
SYMIG	42	-3578.9362	7241.8725	0.0000	1.0000
SYMI	41	-3582.4653	7246.9306	0.0000	1.0000
K2PG	37	-3587.0253	7248.0507	0.0000	1.0000
K2PIG	38	-3586.4779	7248.9558	0.0000	1.0000
K2PI	37	-3590.3989	7254.7977	0.0000	1.0000
GTR	43	-3621.2011	7328.4021	0.0000	1.0000
HKY	39	-3631.5932	7341.1863	0.0000	1.0000
SYM	40	-3634.5814	7349.1629	0.0000	1.0000
K2P	36	-3642.1574	7356.3148	0.0000	1.0000
F81G	39	-3682.8400	7443.6800	0.0000	1.0000
F81IG	40	-3682.4305	7444.8609	0.0000	1.0000
F81I	39	-3686.0231	7450.0462	0.0000	1.0000
JC69G	36	-3690.3922	7452.7844	0.0000	1.0000
JC69IG	37	-3689.9546	7453.9091	0.0000	1.0000
JC69I	36	-3693.6534	7459.3067	0.0000	1.0000
F81	38	-3735.0737	7546.1474	0.0000	1.0000
JC69	35	-3743.2280	7556.4561	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3587.0253	7434.2578	0.6815	0.6815
HKYG	40	-3577.5860	7436.4769	0.2247	0.9061
K2PIG	38	-3586.4779	7440.1955	0.0350	0.9411
K2PI	37	-3590.3989	7441.0048	0.0234	0.9645
GTRG	44	-3566.3025	7442.0405	0.0139	0.9784
HKYIG	41	-3577.1366	7442.6108	0.0105	0.9889
HKYI	40	-3580.8618	7443.0287	0.0085	0.9973
SYMG	41	-3579.2885	7446.9145	0.0012	0.9986
GTRI	44	-3569.1768	7447.7891	0.0008	0.9993
GTRIG	45	-3566.0154	7448.4989	0.0006	0.9999
SYMIG	42	-3578.9362	7453.2427	0.0001	0.9999
SYMI	41	-3582.4653	7453.2682	0.0001	1.0000
HKY	39	-3631.5932	7537.4587	0.0000	1.0000
K2P	36	-3642.1574	7537.4893	0.0000	1.0000
GTR	43	-3621.2011	7544.8049	0.0000	1.0000
SYM	40	-3634.5814	7550.4678	0.0000	1.0000
JC69G	36	-3690.3922	7633.9588	0.0000	1.0000
F81G	39	-3682.8400	7639.9523	0.0000	1.0000
JC69IG	37	-3689.9546	7640.1162	0.0000	1.0000
JC69I	36	-3693.6534	7640.4812	0.0000	1.0000
F81IG	40	-3682.4305	7646.1659	0.0000	1.0000
F81I	39	-3686.0231	7646.3185	0.0000	1.0000
JC69	35	-3743.2280	7732.5979	0.0000	1.0000
F81	38	-3735.0737	7737.3871	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_15412.phylip = 1 - 1133;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15412.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15412.phylip = 1 - 1133;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15412.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 BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15412.phylip = 1 - 1133;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_15412.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;


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End of Output

