
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:04 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/chr2_4315.phylip" (19 taxa, 983 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: SYMG


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
SYMG	41	-3146.2146	6378.0891	0.5281	0.5281
SYMIG	42	-3145.4130	6378.6686	0.3953	0.9234
GTRG	44	-3145.4797	6383.1811	0.0414	0.9648
GTRIG	45	-3144.6933	6383.8050	0.0303	0.9951
SYMI	41	-3150.9654	6387.5907	0.0046	0.9997
GTRI	44	-3150.3630	6392.9478	0.0003	1.0000
K2PG	37	-3172.0703	6421.1163	0.0000	1.0000
K2PIG	38	-3171.0514	6421.2427	0.0000	1.0000
HKYG	40	-3171.0979	6425.6778	0.0000	1.0000
HKYIG	41	-3170.0323	6425.7246	0.0000	1.0000
K2PI	37	-3176.4378	6429.8512	0.0000	1.0000
HKYI	40	-3175.4365	6434.3549	0.0000	1.0000
JC69G	36	-3203.2329	6481.2818	0.0000	1.0000
JC69IG	37	-3202.3061	6481.5880	0.0000	1.0000
SYM	40	-3199.8023	6483.0865	0.0000	1.0000
F81G	39	-3202.1664	6485.6413	0.0000	1.0000
F81IG	40	-3201.2204	6485.9228	0.0000	1.0000
GTR	43	-3198.7038	6487.4374	0.0000	1.0000
JC69I	36	-3207.7720	6490.3600	0.0000	1.0000
F81I	39	-3206.7043	6494.7171	0.0000	1.0000
K2P	36	-3227.4914	6529.7990	0.0000	1.0000
HKY	39	-3226.6630	6534.6346	0.0000	1.0000
JC69	35	-3256.4929	6585.6468	0.0000	1.0000
F81	38	-3255.6048	6590.3495	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-3146.2146	6374.4292	0.4958	0.4958
SYMIG	42	-3145.4130	6374.8261	0.4065	0.9023
GTRG	44	-3145.4797	6378.9594	0.0515	0.9538
GTRIG	45	-3144.6933	6379.3867	0.0416	0.9953
SYMI	41	-3150.9654	6383.9308	0.0043	0.9996
GTRI	44	-3150.3630	6388.7260	0.0004	1.0000
K2PIG	38	-3171.0514	6418.1029	0.0000	1.0000
K2PG	37	-3172.0703	6418.1406	0.0000	1.0000
HKYIG	41	-3170.0323	6422.0646	0.0000	1.0000
HKYG	40	-3171.0979	6422.1959	0.0000	1.0000
K2PI	37	-3176.4378	6426.8755	0.0000	1.0000
HKYI	40	-3175.4365	6430.8730	0.0000	1.0000
JC69G	36	-3203.2329	6478.4657	0.0000	1.0000
JC69IG	37	-3202.3061	6478.6123	0.0000	1.0000
SYM	40	-3199.8023	6479.6045	0.0000	1.0000
F81G	39	-3202.1664	6482.3327	0.0000	1.0000
F81IG	40	-3201.2204	6482.4408	0.0000	1.0000
GTR	43	-3198.7038	6483.4076	0.0000	1.0000
JC69I	36	-3207.7720	6487.5439	0.0000	1.0000
F81I	39	-3206.7043	6491.4085	0.0000	1.0000
K2P	36	-3227.4914	6526.9829	0.0000	1.0000
HKY	39	-3226.6630	6531.3260	0.0000	1.0000
JC69	35	-3256.4929	6582.9858	0.0000	1.0000
F81	38	-3255.6048	6587.2097	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
SYMG	41	-3146.2146	6574.9442	0.9261	0.9261
SYMIG	42	-3145.4130	6580.2317	0.0658	0.9919
SYMI	41	-3150.9654	6584.4458	0.0080	0.9999
GTRG	44	-3145.4797	6594.1462	0.0001	1.0000
K2PG	37	-3172.0703	6599.0931	0.0000	1.0000
GTRIG	45	-3144.6933	6599.4641	0.0000	1.0000
GTRI	44	-3150.3630	6603.9128	0.0000	1.0000
K2PIG	38	-3171.0514	6603.9460	0.0000	1.0000
K2PI	37	-3176.4378	6607.8281	0.0000	1.0000
HKYG	40	-3171.0979	6617.8202	0.0000	1.0000
HKYIG	41	-3170.0323	6622.5796	0.0000	1.0000
HKYI	40	-3175.4365	6626.4973	0.0000	1.0000
JC69G	36	-3203.2329	6654.5276	0.0000	1.0000
JC69IG	37	-3202.3061	6659.5648	0.0000	1.0000
JC69I	36	-3207.7720	6663.6058	0.0000	1.0000
F81G	39	-3202.1664	6673.0665	0.0000	1.0000
SYM	40	-3199.8023	6675.2289	0.0000	1.0000
F81IG	40	-3201.2204	6678.0652	0.0000	1.0000
F81I	39	-3206.7043	6682.1423	0.0000	1.0000
GTR	43	-3198.7038	6693.7038	0.0000	1.0000
K2P	36	-3227.4914	6703.0448	0.0000	1.0000
HKY	39	-3226.6630	6722.0598	0.0000	1.0000
JC69	35	-3256.4929	6754.1571	0.0000	1.0000
F81	38	-3255.6048	6773.0528	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.phylip = 1 - 983;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.phylip = 1 - 983;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (SYMG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.phylip = 1 - 983;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_4315.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=Fixed(Equal);
END;


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End of Output

