
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:00 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_3118.phylip" (19 taxa, 605 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	-1786.0770	3667.2255	0.6307	0.6307
GTRIG	45	-1785.6291	3668.6644	0.3071	0.9378
HKYG	40	-1793.9707	3673.7570	0.0241	0.9619
GTRI	44	-1789.3760	3673.8234	0.0233	0.9852
HKYIG	41	-1793.8437	3675.8046	0.0086	0.9938
HKYI	40	-1795.3270	3676.4697	0.0062	1.0000
K2PG	37	-1811.2745	3701.5085	0.0000	1.0000
K2PIG	38	-1812.0844	3705.4056	0.0000	1.0000
K2PI	37	-1813.7305	3706.4205	0.0000	1.0000
SYMG	41	-1810.5406	3709.1984	0.0000	1.0000
SYMIG	42	-1811.2227	3712.8725	0.0000	1.0000
SYMI	41	-1812.8246	3713.7664	0.0000	1.0000
HKY	39	-1817.0982	3717.7186	0.0000	1.0000
GTR	43	-1812.8475	3718.4401	0.0000	1.0000
F81G	39	-1824.2122	3731.9466	0.0000	1.0000
F81IG	40	-1823.8835	3733.5825	0.0000	1.0000
F81I	39	-1825.1658	3733.8538	0.0000	1.0000
K2P	36	-1836.2582	3749.2065	0.0000	1.0000
SYM	40	-1834.6857	3755.1870	0.0000	1.0000
JC69I	36	-1840.6725	3758.0350	0.0000	1.0000
JC69G	36	-1841.3766	3759.4434	0.0000	1.0000
JC69IG	37	-1842.0379	3763.0353	0.0000	1.0000
F81	38	-1846.1013	3773.4393	0.0000	1.0000
JC69	35	-1864.0631	3802.5551	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1786.0770	3660.1541	0.6072	0.6072
GTRIG	45	-1785.6291	3661.2583	0.3496	0.9569
GTRI	44	-1789.3760	3666.7520	0.0224	0.9793
HKYG	40	-1793.9707	3667.9414	0.0124	0.9916
HKYIG	41	-1793.8437	3669.6874	0.0052	0.9968
HKYI	40	-1795.3270	3670.6541	0.0032	1.0000
K2PG	37	-1811.2745	3696.5490	0.0000	1.0000
K2PIG	38	-1812.0844	3700.1689	0.0000	1.0000
K2PI	37	-1813.7305	3701.4610	0.0000	1.0000
SYMG	41	-1810.5406	3703.0811	0.0000	1.0000
SYMIG	42	-1811.2227	3706.4454	0.0000	1.0000
SYMI	41	-1812.8246	3707.6492	0.0000	1.0000
GTR	43	-1812.8475	3711.6950	0.0000	1.0000
HKY	39	-1817.0982	3712.1965	0.0000	1.0000
F81G	39	-1824.2122	3726.4245	0.0000	1.0000
F81IG	40	-1823.8835	3727.7669	0.0000	1.0000
F81I	39	-1825.1658	3728.3317	0.0000	1.0000
K2P	36	-1836.2582	3744.5163	0.0000	1.0000
SYM	40	-1834.6857	3749.3714	0.0000	1.0000
JC69I	36	-1840.6725	3753.3449	0.0000	1.0000
JC69G	36	-1841.3766	3754.7532	0.0000	1.0000
JC69IG	37	-1842.0379	3758.0759	0.0000	1.0000
F81	38	-1846.1013	3768.2026	0.0000	1.0000
JC69	35	-1864.0631	3798.1263	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1793.9707	3844.1506	0.7620	0.7620
HKYI	40	-1795.3270	3846.8632	0.1963	0.9583
HKYIG	41	-1793.8437	3850.3018	0.0352	0.9935
GTRG	44	-1786.0770	3853.9841	0.0056	0.9991
GTRIG	45	-1785.6291	3859.4936	0.0004	0.9994
K2PG	37	-1811.2745	3859.5425	0.0003	0.9998
GTRI	44	-1789.3760	3860.5820	0.0002	1.0000
K2PI	37	-1813.7305	3864.4545	0.0000	1.0000
K2PIG	38	-1812.0844	3867.5675	0.0000	1.0000
SYMG	41	-1810.5406	3883.6955	0.0000	1.0000
HKY	39	-1817.0982	3884.0004	0.0000	1.0000
SYMI	41	-1812.8246	3888.2636	0.0000	1.0000
SYMIG	42	-1811.2227	3891.4650	0.0000	1.0000
F81G	39	-1824.2122	3898.2284	0.0000	1.0000
F81I	39	-1825.1658	3900.1356	0.0000	1.0000
GTR	43	-1812.8475	3901.1198	0.0000	1.0000
K2P	36	-1836.2582	3903.1046	0.0000	1.0000
F81IG	40	-1823.8835	3903.9761	0.0000	1.0000
JC69I	36	-1840.6725	3911.9331	0.0000	1.0000
JC69G	36	-1841.3766	3913.3414	0.0000	1.0000
JC69IG	37	-1842.0379	3921.0693	0.0000	1.0000
SYM	40	-1834.6857	3925.5805	0.0000	1.0000
F81	38	-1846.1013	3935.6013	0.0000	1.0000
JC69	35	-1864.0631	3952.3093	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_3118.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3118.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_3118.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3118.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_3118.phylip = 1 - 605;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3118.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

