
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:08 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/chr11_3508.phylip" (19 taxa, 639 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: GTRG


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
GTRIG	45	-1770.8501	3638.6818	0.6205	0.6205
GTRG	44	-1772.6633	3639.9932	0.3221	0.9426
GTRI	44	-1774.3885	3643.4437	0.0574	1.0000
HKYIG	41	-1785.7933	3659.3554	0.0000	1.0000
HKYG	40	-1787.1506	3659.7861	0.0000	1.0000
HKYI	40	-1788.6818	3662.8486	0.0000	1.0000
SYMIG	42	-1790.4404	3670.9411	0.0000	1.0000
SYMG	41	-1792.1151	3671.9991	0.0000	1.0000
SYMI	41	-1793.9120	3675.5928	0.0000	1.0000
K2PG	37	-1801.7130	3682.1049	0.0000	1.0000
K2PIG	38	-1804.0192	3688.9783	0.0000	1.0000
K2PI	37	-1807.3454	3693.3697	0.0000	1.0000
GTR	43	-1807.6040	3707.5676	0.0000	1.0000
HKY	39	-1818.4783	3720.1652	0.0000	1.0000
F81IG	40	-1823.2333	3731.9515	0.0000	1.0000
F81G	39	-1824.4418	3732.0923	0.0000	1.0000
SYM	40	-1823.7979	3733.0807	0.0000	1.0000
F81I	39	-1825.9131	3735.0348	0.0000	1.0000
K2P	36	-1832.3341	3741.0935	0.0000	1.0000
JC69IG	37	-1835.2722	3749.2232	0.0000	1.0000
JC69G	36	-1836.5303	3749.4858	0.0000	1.0000
JC69I	36	-1838.0945	3752.6142	0.0000	1.0000
F81	38	-1854.7258	3790.3915	0.0000	1.0000
JC69	35	-1866.4354	3807.0499	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1770.8501	3631.7003	0.6568	0.6568
GTRG	44	-1772.6633	3633.3265	0.2913	0.9481
GTRI	44	-1774.3885	3636.7771	0.0519	1.0000
HKYIG	41	-1785.7933	3653.5866	0.0000	1.0000
HKYG	40	-1787.1506	3654.3012	0.0000	1.0000
HKYI	40	-1788.6818	3657.3637	0.0000	1.0000
SYMIG	42	-1790.4404	3664.8807	0.0000	1.0000
SYMG	41	-1792.1151	3666.2303	0.0000	1.0000
SYMI	41	-1793.9120	3669.8240	0.0000	1.0000
K2PG	37	-1801.7130	3677.4260	0.0000	1.0000
K2PIG	38	-1804.0192	3684.0383	0.0000	1.0000
K2PI	37	-1807.3454	3688.6908	0.0000	1.0000
GTR	43	-1807.6040	3701.2079	0.0000	1.0000
HKY	39	-1818.4783	3714.9566	0.0000	1.0000
F81IG	40	-1823.2333	3726.4666	0.0000	1.0000
F81G	39	-1824.4418	3726.8836	0.0000	1.0000
SYM	40	-1823.7979	3727.5958	0.0000	1.0000
F81I	39	-1825.9131	3729.8261	0.0000	1.0000
K2P	36	-1832.3341	3736.6683	0.0000	1.0000
JC69IG	37	-1835.2722	3744.5444	0.0000	1.0000
JC69G	36	-1836.5303	3745.0606	0.0000	1.0000
JC69I	36	-1838.0945	3748.1890	0.0000	1.0000
F81	38	-1854.7258	3785.4515	0.0000	1.0000
JC69	35	-1866.4354	3802.8708	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1772.6633	3829.5623	0.5855	0.5855
GTRIG	45	-1770.8501	3832.3960	0.1420	0.7274
HKYG	40	-1787.1506	3832.6973	0.1221	0.8495
GTRI	44	-1774.3885	3833.0129	0.1043	0.9538
HKYI	40	-1788.6818	3835.7599	0.0264	0.9802
HKYIG	41	-1785.7933	3836.4427	0.0188	0.9990
K2PG	37	-1801.7130	3842.4425	0.0009	0.9999
SYMG	41	-1792.1151	3849.0863	0.0000	1.0000
SYMIG	42	-1790.4404	3852.1967	0.0000	1.0000
SYMI	41	-1793.9120	3852.6801	0.0000	1.0000
K2PIG	38	-1804.0192	3853.5147	0.0000	1.0000
K2PI	37	-1807.3454	3853.7073	0.0000	1.0000
HKY	39	-1818.4783	3888.8928	0.0000	1.0000
GTR	43	-1807.6040	3892.9838	0.0000	1.0000
K2P	36	-1832.3341	3897.2248	0.0000	1.0000
F81G	39	-1824.4418	3900.8199	0.0000	1.0000
F81I	39	-1825.9131	3903.7624	0.0000	1.0000
F81IG	40	-1823.2333	3904.8628	0.0000	1.0000
JC69G	36	-1836.5303	3905.6172	0.0000	1.0000
SYM	40	-1823.7979	3905.9920	0.0000	1.0000
JC69I	36	-1838.0945	3908.7455	0.0000	1.0000
JC69IG	37	-1835.2722	3909.5608	0.0000	1.0000
F81	38	-1854.7258	3954.9279	0.0000	1.0000
JC69	35	-1866.4354	3958.9674	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.phylip = 1 - 639;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3508.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;


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End of Output

