
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:58 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_27308.phylip" (19 taxa, 770 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	-4080.0130	8253.4881	0.7522	0.7522
GTRIG	45	-4079.9980	8255.7142	0.2471	0.9993
HKYG	40	-4091.7611	8268.0214	0.0005	0.9998
HKYIG	41	-4091.7606	8270.2519	0.0002	1.0000
GTRI	44	-4093.2218	8279.9056	0.0000	1.0000
HKYI	40	-4103.4311	8291.3615	0.0000	1.0000
GTR	43	-4144.6827	8380.5776	0.0000	1.0000
HKY	39	-4153.7421	8389.7582	0.0000	1.0000
K2PG	37	-4167.5045	8412.8506	0.0000	1.0000
K2PIG	38	-4167.5077	8415.0702	0.0000	1.0000
SYMG	41	-4166.0187	8418.7681	0.0000	1.0000
SYMIG	42	-4166.0185	8421.0054	0.0000	1.0000
K2PI	37	-4180.2935	8438.4285	0.0000	1.0000
SYMI	41	-4179.5262	8445.7832	0.0000	1.0000
F81G	39	-4191.1457	8464.5653	0.0000	1.0000
F81IG	40	-4191.1486	8466.7966	0.0000	1.0000
F81I	39	-4201.3738	8485.0216	0.0000	1.0000
K2P	36	-4232.4592	8540.5528	0.0000	1.0000
SYM	40	-4232.1851	8548.8694	0.0000	1.0000
JC69G	36	-4244.9121	8565.4587	0.0000	1.0000
JC69IG	37	-4244.9143	8567.6701	0.0000	1.0000
F81	38	-4248.7319	8577.5184	0.0000	1.0000
JC69I	36	-4256.5288	8588.6920	0.0000	1.0000
JC69	35	-4305.8752	8685.1836	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4080.0130	8248.0261	0.7278	0.7278
GTRIG	45	-4079.9980	8249.9960	0.2718	0.9996
HKYG	40	-4091.7611	8263.5221	0.0003	0.9999
HKYIG	41	-4091.7606	8265.5212	0.0001	1.0000
GTRI	44	-4093.2218	8274.4436	0.0000	1.0000
HKYI	40	-4103.4311	8286.8622	0.0000	1.0000
GTR	43	-4144.6827	8375.3654	0.0000	1.0000
HKY	39	-4153.7421	8385.4843	0.0000	1.0000
K2PG	37	-4167.5045	8409.0091	0.0000	1.0000
K2PIG	38	-4167.5077	8411.0155	0.0000	1.0000
SYMG	41	-4166.0187	8414.0373	0.0000	1.0000
SYMIG	42	-4166.0185	8416.0370	0.0000	1.0000
K2PI	37	-4180.2935	8434.5870	0.0000	1.0000
SYMI	41	-4179.5262	8441.0524	0.0000	1.0000
F81G	39	-4191.1457	8460.2914	0.0000	1.0000
F81IG	40	-4191.1486	8462.2973	0.0000	1.0000
F81I	39	-4201.3738	8480.7476	0.0000	1.0000
K2P	36	-4232.4592	8536.9184	0.0000	1.0000
SYM	40	-4232.1851	8544.3701	0.0000	1.0000
JC69G	36	-4244.9121	8561.8243	0.0000	1.0000
JC69IG	37	-4244.9143	8563.8286	0.0000	1.0000
F81	38	-4248.7319	8573.4637	0.0000	1.0000
JC69I	36	-4256.5288	8585.0577	0.0000	1.0000
JC69	35	-4305.8752	8681.7504	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4091.7611	8449.3777	0.7954	0.7954
GTRG	44	-4080.0130	8452.4673	0.1697	0.9651
HKYIG	41	-4091.7606	8456.0232	0.0287	0.9938
GTRIG	45	-4079.9980	8459.0836	0.0062	1.0000
HKYI	40	-4103.4311	8472.7178	0.0000	1.0000
GTRI	44	-4093.2218	8478.8848	0.0000	1.0000
HKY	39	-4153.7421	8566.6935	0.0000	1.0000
GTR	43	-4144.6827	8575.1602	0.0000	1.0000
K2PG	37	-4167.5045	8580.9255	0.0000	1.0000
K2PIG	38	-4167.5077	8587.5783	0.0000	1.0000
SYMG	41	-4166.0187	8604.5393	0.0000	1.0000
K2PI	37	-4180.2935	8606.5034	0.0000	1.0000
SYMIG	42	-4166.0185	8611.1854	0.0000	1.0000
SYMI	41	-4179.5262	8631.5544	0.0000	1.0000
F81G	39	-4191.1457	8641.5006	0.0000	1.0000
F81IG	40	-4191.1486	8648.1529	0.0000	1.0000
F81I	39	-4201.3738	8661.9569	0.0000	1.0000
K2P	36	-4232.4592	8704.1885	0.0000	1.0000
JC69G	36	-4244.9121	8729.0943	0.0000	1.0000
SYM	40	-4232.1851	8730.2257	0.0000	1.0000
JC69IG	37	-4244.9143	8735.7450	0.0000	1.0000
F81	38	-4248.7319	8750.0266	0.0000	1.0000
JC69I	36	-4256.5288	8752.3277	0.0000	1.0000
JC69	35	-4305.8752	8844.3740	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/chr2_27308.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27308.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/chr2_27308.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27308.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/chr2_27308.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27308.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

