
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:27 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/chr3_7243.phylip" (19 taxa, 855 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-3060.4659	6213.8206	0.4730	0.4730
GTRI	44	-3061.0321	6214.9531	0.2685	0.7415
GTRIG	45	-3059.9601	6215.0375	0.2574	0.9989
HKYG	40	-3071.4946	6227.0186	0.0006	0.9996
HKYIG	41	-3071.4544	6229.1449	0.0002	0.9998
HKYI	40	-3072.6730	6229.3754	0.0002	1.0000
SYMI	41	-3095.7829	6277.8019	0.0000	1.0000
SYMG	41	-3096.1168	6278.4698	0.0000	1.0000
SYMIG	42	-3095.4152	6279.2786	0.0000	1.0000
K2PG	37	-3107.2435	6291.9288	0.0000	1.0000
K2PI	37	-3108.1532	6293.7483	0.0000	1.0000
K2PIG	38	-3107.3084	6294.2492	0.0000	1.0000
GTR	43	-3102.8299	6296.3256	0.0000	1.0000
HKY	39	-3113.9709	6309.7700	0.0000	1.0000
SYM	40	-3138.7774	6361.5842	0.0000	1.0000
K2P	36	-3151.1575	6377.5717	0.0000	1.0000
F81G	39	-3173.5220	6428.8723	0.0000	1.0000
F81IG	40	-3173.4810	6430.9914	0.0000	1.0000
F81I	39	-3174.7593	6431.3467	0.0000	1.0000
JC69G	36	-3201.5244	6478.3055	0.0000	1.0000
JC69I	36	-3202.3587	6479.9742	0.0000	1.0000
JC69IG	37	-3201.4539	6480.3497	0.0000	1.0000
F81	38	-3213.5408	6506.7139	0.0000	1.0000
JC69	35	-3241.8701	6556.8172	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3060.4659	6208.9317	0.4589	0.4589
GTRIG	45	-3059.9601	6209.9201	0.2799	0.7388
GTRI	44	-3061.0321	6210.0642	0.2605	0.9993
HKYG	40	-3071.4946	6222.9891	0.0004	0.9997
HKYIG	41	-3071.4544	6224.9087	0.0002	0.9999
HKYI	40	-3072.6730	6225.3459	0.0001	1.0000
SYMI	41	-3095.7829	6273.5657	0.0000	1.0000
SYMG	41	-3096.1168	6274.2337	0.0000	1.0000
SYMIG	42	-3095.4152	6274.8304	0.0000	1.0000
K2PG	37	-3107.2435	6288.4870	0.0000	1.0000
K2PI	37	-3108.1532	6290.3064	0.0000	1.0000
K2PIG	38	-3107.3084	6290.6168	0.0000	1.0000
GTR	43	-3102.8299	6291.6598	0.0000	1.0000
HKY	39	-3113.9709	6305.9418	0.0000	1.0000
SYM	40	-3138.7774	6357.5547	0.0000	1.0000
K2P	36	-3151.1575	6374.3150	0.0000	1.0000
F81G	39	-3173.5220	6425.0441	0.0000	1.0000
F81IG	40	-3173.4810	6426.9619	0.0000	1.0000
F81I	39	-3174.7593	6427.5185	0.0000	1.0000
JC69G	36	-3201.5244	6475.0488	0.0000	1.0000
JC69I	36	-3202.3587	6476.7174	0.0000	1.0000
JC69IG	37	-3201.4539	6476.9079	0.0000	1.0000
F81	38	-3213.5408	6503.0816	0.0000	1.0000
JC69	35	-3241.8701	6553.7402	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3071.4946	6413.0332	0.6755	0.6755
HKYI	40	-3072.6730	6415.3900	0.2079	0.8835
GTRG	44	-3060.4659	6417.9802	0.0569	0.9404
GTRI	44	-3061.0321	6419.1127	0.0323	0.9727
HKYIG	41	-3071.4544	6419.7039	0.0241	0.9968
GTRIG	45	-3059.9601	6423.7197	0.0032	1.0000
K2PG	37	-3107.2435	6464.2777	0.0000	1.0000
K2PI	37	-3108.1532	6466.0972	0.0000	1.0000
SYMI	41	-3095.7829	6468.3609	0.0000	1.0000
SYMG	41	-3096.1168	6469.0288	0.0000	1.0000
K2PIG	38	-3107.3084	6471.1587	0.0000	1.0000
SYMIG	42	-3095.4152	6474.3766	0.0000	1.0000
HKY	39	-3113.9709	6491.2347	0.0000	1.0000
GTR	43	-3102.8299	6495.9572	0.0000	1.0000
K2P	36	-3151.1575	6545.3547	0.0000	1.0000
SYM	40	-3138.7774	6547.5988	0.0000	1.0000
F81G	39	-3173.5220	6610.3370	0.0000	1.0000
F81I	39	-3174.7593	6612.8115	0.0000	1.0000
F81IG	40	-3173.4810	6617.0060	0.0000	1.0000
JC69G	36	-3201.5244	6646.0885	0.0000	1.0000
JC69I	36	-3202.3587	6647.7571	0.0000	1.0000
JC69IG	37	-3201.4539	6652.6986	0.0000	1.0000
F81	38	-3213.5408	6683.6234	0.0000	1.0000
JC69	35	-3241.8701	6720.0288	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/chr3_7243.phylip = 1 - 855;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7243.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/chr3_7243.phylip = 1 - 855;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7243.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7243.phylip = 1 - 855;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7243.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

