
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:49 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_2724.phylip" (19 taxa, 545 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1589.4581	3265.4241	0.4341	0.4341
GTRG	44	-1585.2183	3266.3566	0.2723	0.7064
HKYI	40	-1590.3784	3267.2647	0.1729	0.8793
HKYIG	41	-1590.4069	3269.6607	0.0522	0.9315
GTRIG	45	-1585.8047	3269.9060	0.0462	0.9776
GTRI	44	-1587.7173	3271.3546	0.0224	1.0000
SYMG	41	-1604.5756	3297.9981	0.0000	1.0000
SYMIG	42	-1603.7509	3298.6971	0.0000	1.0000
SYMI	41	-1605.9584	3300.7637	0.0000	1.0000
K2PG	37	-1611.0178	3301.5819	0.0000	1.0000
K2PIG	38	-1609.9820	3301.8218	0.0000	1.0000
K2PI	37	-1611.4016	3302.3496	0.0000	1.0000
GTR	43	-1617.1790	3327.9109	0.0000	1.0000
HKY	39	-1623.1936	3330.5654	0.0000	1.0000
SYM	40	-1636.0544	3358.6168	0.0000	1.0000
F81G	39	-1638.7002	3361.5786	0.0000	1.0000
K2P	36	-1642.3803	3362.0048	0.0000	1.0000
F81I	39	-1639.3365	3362.8511	0.0000	1.0000
F81IG	40	-1638.5443	3363.5966	0.0000	1.0000
JC69G	36	-1654.8978	3387.0397	0.0000	1.0000
JC69I	36	-1655.3081	3387.8603	0.0000	1.0000
JC69IG	37	-1654.6610	3388.8683	0.0000	1.0000
F81	38	-1668.4238	3418.7053	0.0000	1.0000
JC69	35	-1684.4428	3443.8364	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1585.2183	3258.4366	0.4001	0.4001
HKYG	40	-1589.4581	3258.9161	0.3148	0.7150
HKYI	40	-1590.3784	3260.7568	0.1254	0.8404
GTRIG	45	-1585.8047	3261.6094	0.0819	0.9223
HKYIG	41	-1590.4069	3262.8138	0.0448	0.9671
GTRI	44	-1587.7173	3263.4346	0.0329	1.0000
SYMG	41	-1604.5756	3291.1512	0.0000	1.0000
SYMIG	42	-1603.7509	3291.5018	0.0000	1.0000
SYMI	41	-1605.9584	3293.9168	0.0000	1.0000
K2PIG	38	-1609.9820	3295.9641	0.0000	1.0000
K2PG	37	-1611.0178	3296.0355	0.0000	1.0000
K2PI	37	-1611.4016	3296.8033	0.0000	1.0000
GTR	43	-1617.1790	3320.3580	0.0000	1.0000
HKY	39	-1623.1936	3324.3872	0.0000	1.0000
SYM	40	-1636.0544	3352.1089	0.0000	1.0000
F81G	39	-1638.7002	3355.4004	0.0000	1.0000
F81I	39	-1639.3365	3356.6729	0.0000	1.0000
K2P	36	-1642.3803	3356.7607	0.0000	1.0000
F81IG	40	-1638.5443	3357.0887	0.0000	1.0000
JC69G	36	-1654.8978	3381.7956	0.0000	1.0000
JC69I	36	-1655.3081	3382.6162	0.0000	1.0000
JC69IG	37	-1654.6610	3383.3219	0.0000	1.0000
F81	38	-1668.4238	3412.8476	0.0000	1.0000
JC69	35	-1684.4428	3438.8855	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1589.4581	3430.9476	0.7066	0.7066
HKYI	40	-1590.3784	3432.7882	0.2815	0.9881
HKYIG	41	-1590.4069	3439.1460	0.0117	0.9998
GTRG	44	-1585.2183	3447.6712	0.0002	1.0000
GTRI	44	-1587.7173	3452.6692	0.0000	1.0000
GTRIG	45	-1585.8047	3455.1447	0.0000	1.0000
K2PG	37	-1611.0178	3455.1646	0.0000	1.0000
K2PI	37	-1611.4016	3455.9323	0.0000	1.0000
K2PIG	38	-1609.9820	3459.3939	0.0000	1.0000
SYMG	41	-1604.5756	3467.4834	0.0000	1.0000
SYMI	41	-1605.9584	3470.2490	0.0000	1.0000
SYMIG	42	-1603.7509	3472.1348	0.0000	1.0000
HKY	39	-1623.1936	3492.1178	0.0000	1.0000
GTR	43	-1617.1790	3505.2918	0.0000	1.0000
K2P	36	-1642.3803	3511.5890	0.0000	1.0000
F81G	39	-1638.7002	3523.1310	0.0000	1.0000
SYM	40	-1636.0544	3524.1403	0.0000	1.0000
F81I	39	-1639.3365	3524.4036	0.0000	1.0000
F81IG	40	-1638.5443	3529.1201	0.0000	1.0000
JC69G	36	-1654.8978	3536.6239	0.0000	1.0000
JC69I	36	-1655.3081	3537.4444	0.0000	1.0000
JC69IG	37	-1654.6610	3542.4510	0.0000	1.0000
F81	38	-1668.4238	3576.2775	0.0000	1.0000
JC69	35	-1684.4428	3589.4130	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_2724.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2724.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2724.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2724.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;


[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_2724.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2724.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

