
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:51 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_2735.phylip" (19 taxa, 705 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	-1767.9194	3629.8389	0.4258	0.4258
GTRI	44	-1768.2073	3630.4146	0.3193	0.7451
GTRIG	45	-1767.7140	3631.7101	0.1671	0.9122
HKYG	40	-1774.8032	3634.5461	0.0405	0.9526
HKYI	40	-1775.0508	3635.0413	0.0316	0.9842
HKYIG	41	-1774.6172	3636.4289	0.0158	1.0000
GTR	43	-1790.1510	3672.0266	0.0000	1.0000
HKY	39	-1796.8537	3676.3991	0.0000	1.0000
F81G	39	-1810.3447	3703.3812	0.0000	1.0000
F81I	39	-1810.5971	3703.8859	0.0000	1.0000
F81IG	40	-1810.1569	3705.2536	0.0000	1.0000
K2PG	37	-1815.0460	3708.3079	0.0000	1.0000
SYMG	41	-1810.5922	3708.3790	0.0000	1.0000
K2PI	37	-1815.3024	3708.8207	0.0000	1.0000
SYMI	41	-1810.8989	3708.9923	0.0000	1.0000
K2PIG	38	-1814.7684	3709.9872	0.0000	1.0000
SYMIG	42	-1810.3127	3710.0816	0.0000	1.0000
F81	38	-1832.4436	3745.3376	0.0000	1.0000
SYM	40	-1833.3955	3751.7307	0.0000	1.0000
K2P	36	-1838.2199	3752.4279	0.0000	1.0000
JC69G	36	-1846.3474	3768.6828	0.0000	1.0000
JC69I	36	-1846.6096	3769.2073	0.0000	1.0000
JC69IG	37	-1846.1212	3770.4583	0.0000	1.0000
JC69	35	-1868.9947	3811.7562	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1767.9194	3623.8389	0.4299	0.4299
GTRI	44	-1768.2073	3624.4146	0.3224	0.7523
GTRIG	45	-1767.7140	3625.4279	0.1942	0.9465
HKYG	40	-1774.8032	3629.6064	0.0240	0.9706
HKYI	40	-1775.0508	3630.1015	0.0188	0.9893
HKYIG	41	-1774.6172	3631.2343	0.0107	1.0000
GTR	43	-1790.1510	3666.3019	0.0000	1.0000
HKY	39	-1796.8537	3671.7074	0.0000	1.0000
F81G	39	-1810.3447	3698.6895	0.0000	1.0000
F81I	39	-1810.5971	3699.1942	0.0000	1.0000
F81IG	40	-1810.1569	3700.3138	0.0000	1.0000
SYMG	41	-1810.5922	3703.1844	0.0000	1.0000
SYMI	41	-1810.8989	3703.7978	0.0000	1.0000
K2PG	37	-1815.0460	3704.0920	0.0000	1.0000
K2PI	37	-1815.3024	3704.6048	0.0000	1.0000
SYMIG	42	-1810.3127	3704.6254	0.0000	1.0000
K2PIG	38	-1814.7684	3705.5368	0.0000	1.0000
F81	38	-1832.4436	3740.8871	0.0000	1.0000
SYM	40	-1833.3955	3746.7909	0.0000	1.0000
K2P	36	-1838.2199	3748.4399	0.0000	1.0000
JC69G	36	-1846.3474	3764.6948	0.0000	1.0000
JC69I	36	-1846.6096	3765.2193	0.0000	1.0000
JC69IG	37	-1846.1212	3766.2424	0.0000	1.0000
JC69	35	-1868.9947	3807.9894	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1774.8032	3811.9343	0.5466	0.5466
HKYI	40	-1775.0508	3812.4294	0.4267	0.9733
HKYIG	41	-1774.6172	3818.1204	0.0248	0.9981
GTRG	44	-1767.9194	3824.3996	0.0011	0.9991
GTRI	44	-1768.2073	3824.9753	0.0008	1.0000
GTRIG	45	-1767.7140	3830.5468	0.0000	1.0000
HKY	39	-1796.8537	3849.4771	0.0000	1.0000
GTR	43	-1790.1510	3862.3044	0.0000	1.0000
K2PG	37	-1815.0460	3872.7454	0.0000	1.0000
K2PI	37	-1815.3024	3873.2581	0.0000	1.0000
F81G	39	-1810.3447	3876.4592	0.0000	1.0000
F81I	39	-1810.5971	3876.9639	0.0000	1.0000
K2PIG	38	-1814.7684	3878.7483	0.0000	1.0000
F81IG	40	-1810.1569	3882.6417	0.0000	1.0000
SYMG	41	-1810.5922	3890.0705	0.0000	1.0000
SYMI	41	-1810.8989	3890.6839	0.0000	1.0000
SYMIG	42	-1810.3127	3896.0697	0.0000	1.0000
K2P	36	-1838.2199	3912.5350	0.0000	1.0000
F81	38	-1832.4436	3914.0986	0.0000	1.0000
JC69G	36	-1846.3474	3928.7899	0.0000	1.0000
SYM	40	-1833.3955	3929.1188	0.0000	1.0000
JC69I	36	-1846.6096	3929.3144	0.0000	1.0000
JC69IG	37	-1846.1212	3934.8957	0.0000	1.0000
JC69	35	-1868.9947	3967.5263	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_2735.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2735.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_2735.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2735.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_2735.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2735.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

