
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:17 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_11796.phylip" (19 taxa, 827 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	-3276.9324	6646.9288	0.6811	0.6811
GTRIG	45	-3276.6734	6648.6478	0.2884	0.9695
HKYG	40	-3284.8440	6653.8610	0.0213	0.9908
HKYIG	41	-3284.6530	6655.6934	0.0085	0.9993
GTRI	44	-3283.8214	6660.7067	0.0007	1.0000
HKYI	40	-3291.4012	6666.9754	0.0000	1.0000
GTR	43	-3328.8803	6748.5932	0.0000	1.0000
HKY	39	-3334.9776	6751.9195	0.0000	1.0000
SYMG	41	-3341.0455	6768.4783	0.0000	1.0000
K2PG	37	-3345.9242	6769.4123	0.0000	1.0000
SYMIG	42	-3340.9991	6770.6053	0.0000	1.0000
K2PIG	38	-3345.8473	6771.4560	0.0000	1.0000
SYMI	41	-3348.2048	6782.7968	0.0000	1.0000
K2PI	37	-3352.8557	6783.2755	0.0000	1.0000
SYM	40	-3385.4527	6855.0783	0.0000	1.0000
K2P	36	-3391.5805	6858.5331	0.0000	1.0000
F81G	39	-3401.6096	6885.1837	0.0000	1.0000
F81IG	40	-3401.5289	6887.2309	0.0000	1.0000
F81I	39	-3407.4401	6896.8446	0.0000	1.0000
JC69G	36	-3443.6735	6962.7192	0.0000	1.0000
JC69IG	37	-3443.6236	6964.8113	0.0000	1.0000
F81	38	-3442.9098	6965.5810	0.0000	1.0000
JC69I	36	-3449.8070	6974.9861	0.0000	1.0000
JC69	35	-3484.4949	7042.1757	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3276.9324	6641.8649	0.6637	0.6637
GTRIG	45	-3276.6734	6643.3469	0.3164	0.9801
HKYG	40	-3284.8440	6649.6880	0.0133	0.9934
HKYIG	41	-3284.6530	6651.3061	0.0059	0.9993
GTRI	44	-3283.8214	6655.6427	0.0007	1.0000
HKYI	40	-3291.4012	6662.8024	0.0000	1.0000
GTR	43	-3328.8803	6743.7605	0.0000	1.0000
HKY	39	-3334.9776	6747.9551	0.0000	1.0000
SYMG	41	-3341.0455	6764.0910	0.0000	1.0000
K2PG	37	-3345.9242	6765.8483	0.0000	1.0000
SYMIG	42	-3340.9991	6765.9981	0.0000	1.0000
K2PIG	38	-3345.8473	6767.6946	0.0000	1.0000
SYMI	41	-3348.2048	6778.4095	0.0000	1.0000
K2PI	37	-3352.8557	6779.7115	0.0000	1.0000
SYM	40	-3385.4527	6850.9053	0.0000	1.0000
K2P	36	-3391.5805	6855.1610	0.0000	1.0000
F81G	39	-3401.6096	6881.2192	0.0000	1.0000
F81IG	40	-3401.5289	6883.0579	0.0000	1.0000
F81I	39	-3407.4401	6892.8802	0.0000	1.0000
JC69G	36	-3443.6735	6959.3471	0.0000	1.0000
JC69IG	37	-3443.6236	6961.2473	0.0000	1.0000
F81	38	-3442.9098	6961.8196	0.0000	1.0000
JC69I	36	-3449.8070	6971.6140	0.0000	1.0000
JC69	35	-3484.4949	7038.9899	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3284.8440	6838.4002	0.9545	0.9545
HKYIG	41	-3284.6530	6844.7361	0.0402	0.9947
GTRG	44	-3276.9324	6849.4483	0.0038	0.9985
HKYI	40	-3291.4012	6851.5145	0.0014	0.9998
GTRIG	45	-3276.6734	6855.6481	0.0002	1.0000
GTRI	44	-3283.8214	6863.2261	0.0000	1.0000
HKY	39	-3334.9776	6931.9495	0.0000	1.0000
K2PG	37	-3345.9242	6940.4071	0.0000	1.0000
GTR	43	-3328.8803	6946.6261	0.0000	1.0000
K2PIG	38	-3345.8473	6946.9712	0.0000	1.0000
K2PI	37	-3352.8557	6954.2702	0.0000	1.0000
SYMG	41	-3341.0455	6957.5210	0.0000	1.0000
SYMIG	42	-3340.9991	6964.1459	0.0000	1.0000
SYMI	41	-3348.2048	6971.8395	0.0000	1.0000
K2P	36	-3391.5805	7025.0019	0.0000	1.0000
SYM	40	-3385.4527	7039.6175	0.0000	1.0000
F81G	39	-3401.6096	7065.2136	0.0000	1.0000
F81IG	40	-3401.5289	7071.7701	0.0000	1.0000
F81I	39	-3407.4401	7076.8746	0.0000	1.0000
JC69G	36	-3443.6735	7129.1880	0.0000	1.0000
JC69IG	37	-3443.6236	7135.8060	0.0000	1.0000
F81	38	-3442.9098	7141.0962	0.0000	1.0000
JC69I	36	-3449.8070	7141.4549	0.0000	1.0000
JC69	35	-3484.4949	7204.1131	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_11796.phylip = 1 - 827;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_11796.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_11796.phylip = 1 - 827;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_11796.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_11796.phylip = 1 - 827;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_11796.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

