
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:34 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/chr4_7064.phylip" (19 taxa, 785 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-3352.6529	6791.9411	0.4713	0.4713
HKYG	40	-3353.9251	6792.2589	0.4020	0.8733
GTRIG	45	-3350.4783	6796.5588	0.0468	0.9201
HKYI	40	-3356.1359	6796.6803	0.0441	0.9642
GTRG	44	-3351.9583	6797.2680	0.0328	0.9970
GTRI	44	-3354.3666	6802.0846	0.0030	1.0000
K2PG	37	-3400.6259	6879.0161	0.0000	1.0000
K2PIG	38	-3399.5641	6879.1015	0.0000	1.0000
K2PI	37	-3402.3437	6882.4518	0.0000	1.0000
SYMG	41	-3398.2092	6883.0537	0.0000	1.0000
SYMIG	42	-3397.2991	6883.4661	0.0000	1.0000
SYMI	41	-3400.4783	6887.5918	0.0000	1.0000
HKY	39	-3442.0566	6966.3012	0.0000	1.0000
GTR	43	-3440.4095	6971.9255	0.0000	1.0000
F81IG	40	-3466.5361	7017.4809	0.0000	1.0000
F81G	39	-3467.7282	7017.6443	0.0000	1.0000
F81I	39	-3468.6029	7019.3937	0.0000	1.0000
K2P	36	-3484.9954	7045.5523	0.0000	1.0000
SYM	40	-3481.7309	7047.8703	0.0000	1.0000
JC69G	36	-3497.1341	7069.8297	0.0000	1.0000
JC69IG	37	-3496.0605	7069.8855	0.0000	1.0000
JC69I	36	-3498.2843	7072.1301	0.0000	1.0000
F81	38	-3547.5147	7175.0027	0.0000	1.0000
JC69	35	-3577.1819	7227.7283	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-3352.6529	6787.3058	0.4728	0.4728
HKYG	40	-3353.9251	6787.8503	0.3601	0.8329
GTRIG	45	-3350.4783	6790.9567	0.0762	0.9091
GTRG	44	-3351.9583	6791.9167	0.0471	0.9563
HKYI	40	-3356.1359	6792.2717	0.0395	0.9958
GTRI	44	-3354.3666	6796.7332	0.0042	1.0000
K2PIG	38	-3399.5641	6875.1283	0.0000	1.0000
K2PG	37	-3400.6259	6875.2517	0.0000	1.0000
SYMG	41	-3398.2092	6878.4184	0.0000	1.0000
SYMIG	42	-3397.2991	6878.5982	0.0000	1.0000
K2PI	37	-3402.3437	6878.6874	0.0000	1.0000
SYMI	41	-3400.4783	6882.9565	0.0000	1.0000
HKY	39	-3442.0566	6962.1132	0.0000	1.0000
GTR	43	-3440.4095	6966.8189	0.0000	1.0000
F81IG	40	-3466.5361	7013.0723	0.0000	1.0000
F81G	39	-3467.7282	7013.4563	0.0000	1.0000
F81I	39	-3468.6029	7015.2058	0.0000	1.0000
K2P	36	-3484.9954	7041.9908	0.0000	1.0000
SYM	40	-3481.7309	7043.4617	0.0000	1.0000
JC69IG	37	-3496.0605	7066.1211	0.0000	1.0000
JC69G	36	-3497.1341	7066.2682	0.0000	1.0000
JC69I	36	-3498.2843	7068.5686	0.0000	1.0000
F81	38	-3547.5147	7171.0295	0.0000	1.0000
JC69	35	-3577.1819	7224.3638	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3353.9251	6974.4776	0.8084	0.8084
HKYIG	41	-3352.6529	6978.5989	0.1030	0.9114
HKYI	40	-3356.1359	6978.8991	0.0886	1.0000
GTRG	44	-3351.9583	6997.2068	0.0000	1.0000
GTRIG	45	-3350.4783	7000.9124	0.0000	1.0000
GTRI	44	-3354.3666	7002.0233	0.0000	1.0000
K2PG	37	-3400.6259	7047.8820	0.0000	1.0000
K2PI	37	-3402.3437	7051.3177	0.0000	1.0000
K2PIG	38	-3399.5641	7052.4243	0.0000	1.0000
SYMG	41	-3398.2092	7069.7115	0.0000	1.0000
SYMI	41	-3400.4783	7074.2496	0.0000	1.0000
SYMIG	42	-3397.2991	7074.5569	0.0000	1.0000
HKY	39	-3442.0566	7144.0749	0.0000	1.0000
GTR	43	-3440.4095	7167.4433	0.0000	1.0000
F81G	39	-3467.7282	7195.4180	0.0000	1.0000
F81I	39	-3468.6029	7197.1675	0.0000	1.0000
F81IG	40	-3466.5361	7199.6996	0.0000	1.0000
K2P	36	-3484.9954	7209.9554	0.0000	1.0000
SYM	40	-3481.7309	7230.0891	0.0000	1.0000
JC69G	36	-3497.1341	7234.2328	0.0000	1.0000
JC69I	36	-3498.2843	7236.5332	0.0000	1.0000
JC69IG	37	-3496.0605	7238.7514	0.0000	1.0000
F81	38	-3547.5147	7348.3255	0.0000	1.0000
JC69	35	-3577.1819	7387.6627	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7064.phylip = 1 - 785;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7064.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7064.phylip = 1 - 785;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7064.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr4_7064.phylip = 1 - 785;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7064.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

