
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:42 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/chr5_14766.phylip" (19 taxa, 494 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: K2PI


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	-1628.9080	3357.0571	0.4853	0.4853
HKYIG	41	-1634.0000	3357.6195	0.3663	0.8516
HKYI	40	-1637.1833	3361.6072	0.0499	0.9015
HKYG	40	-1637.6932	3362.6270	0.0300	0.9314
GTRI	44	-1633.4331	3363.6859	0.0176	0.9491
K2PIG	38	-1640.7381	3363.9904	0.0152	0.9642
SYMIG	42	-1636.0609	3364.1307	0.0141	0.9783
GTRG	44	-1633.7219	3364.2634	0.0132	0.9916
K2PI	37	-1643.1973	3366.5612	0.0042	0.9958
SYMI	41	-1639.2777	3368.1749	0.0019	0.9976
K2PG	37	-1644.1024	3368.3715	0.0017	0.9993
SYMG	41	-1640.2834	3370.1863	0.0007	1.0000
F81IG	40	-1662.7166	3412.6738	0.0000	1.0000
F81G	39	-1665.5654	3416.0030	0.0000	1.0000
JC69IG	37	-1668.7961	3417.7589	0.0000	1.0000
F81I	39	-1666.5726	3418.0174	0.0000	1.0000
JC69G	36	-1671.6809	3421.1911	0.0000	1.0000
JC69I	36	-1672.5468	3422.9229	0.0000	1.0000
GTR	43	-1700.5246	3495.4582	0.0000	1.0000
SYM	40	-1708.3920	3504.0245	0.0000	1.0000
HKY	39	-1709.6540	3504.1803	0.0000	1.0000
K2P	36	-1716.9620	3511.7533	0.0000	1.0000
JC69	35	-1735.0544	3545.6109	0.0000	1.0000
F81	38	-1736.1184	3554.7512	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1628.9080	3347.8160	0.6774	0.6774
HKYIG	41	-1634.0000	3350.0001	0.2273	0.9047
HKYI	40	-1637.1833	3354.3666	0.0256	0.9303
GTRI	44	-1633.4331	3354.8663	0.0199	0.9503
HKYG	40	-1637.6932	3355.3864	0.0154	0.9656
GTRG	44	-1633.7219	3355.4438	0.0149	0.9806
SYMIG	42	-1636.0609	3356.1219	0.0106	0.9912
K2PIG	38	-1640.7381	3357.4761	0.0054	0.9966
K2PI	37	-1643.1973	3360.3946	0.0013	0.9979
SYMI	41	-1639.2777	3360.5555	0.0012	0.9991
K2PG	37	-1644.1024	3362.2048	0.0005	0.9996
SYMG	41	-1640.2834	3362.5669	0.0004	1.0000
F81IG	40	-1662.7166	3405.4331	0.0000	1.0000
F81G	39	-1665.5654	3409.1307	0.0000	1.0000
F81I	39	-1666.5726	3411.1452	0.0000	1.0000
JC69IG	37	-1668.7961	3411.5923	0.0000	1.0000
JC69G	36	-1671.6809	3415.3618	0.0000	1.0000
JC69I	36	-1672.5468	3417.0935	0.0000	1.0000
GTR	43	-1700.5246	3487.0493	0.0000	1.0000
SYM	40	-1708.3920	3496.7839	0.0000	1.0000
HKY	39	-1709.6540	3497.3080	0.0000	1.0000
K2P	36	-1716.9620	3505.9240	0.0000	1.0000
JC69	35	-1735.0544	3540.1088	0.0000	1.0000
F81	38	-1736.1184	3548.2369	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-1643.1973	3515.8884	0.4923	0.4923
K2PIG	38	-1640.7381	3517.1725	0.2590	0.7513
K2PG	37	-1644.1024	3517.6987	0.1991	0.9505
HKYIG	41	-1634.0000	3522.3040	0.0199	0.9704
HKYI	40	-1637.1833	3522.4680	0.0183	0.9887
HKYG	40	-1637.6932	3523.4878	0.0110	0.9997
SYMIG	42	-1636.0609	3532.6284	0.0001	0.9998
SYMI	41	-1639.2777	3532.8594	0.0001	0.9999
SYMG	41	-1640.2834	3534.8708	0.0000	1.0000
GTRIG	45	-1628.9080	3536.9301	0.0000	1.0000
GTRI	44	-1633.4331	3539.7778	0.0000	1.0000
GTRG	44	-1633.7219	3540.3553	0.0000	1.0000
JC69G	36	-1671.6809	3566.6531	0.0000	1.0000
JC69IG	37	-1668.7961	3567.0861	0.0000	1.0000
JC69I	36	-1672.5468	3568.3848	0.0000	1.0000
F81G	39	-1665.5654	3573.0296	0.0000	1.0000
F81IG	40	-1662.7166	3573.5346	0.0000	1.0000
F81I	39	-1666.5726	3575.0440	0.0000	1.0000
K2P	36	-1716.9620	3657.2153	0.0000	1.0000
HKY	39	-1709.6540	3661.2069	0.0000	1.0000
SYM	40	-1708.3920	3664.8853	0.0000	1.0000
GTR	43	-1700.5246	3667.7583	0.0000	1.0000
JC69	35	-1735.0544	3687.1975	0.0000	1.0000
F81	38	-1736.1184	3707.9332	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/chr5_14766.phylip = 1 - 494;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14766.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/chr5_14766.phylip = 1 - 494;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14766.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 (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14766.phylip = 1 - 494;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_14766.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

