
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:08 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/chr3_362.phylip" (19 taxa, 594 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	-1646.6324	3388.4779	0.5318	0.5318
GTRIG	45	-1646.2825	3390.1198	0.2340	0.7658
GTRI	44	-1648.1876	3391.5884	0.1123	0.8781
HKYG	40	-1653.2933	3392.5178	0.0705	0.9487
HKYIG	41	-1652.9840	3394.2071	0.0303	0.9790
HKYI	40	-1654.5035	3394.9382	0.0210	1.0000
K2PG	37	-1669.9291	3418.9158	0.0000	1.0000
K2PIG	38	-1669.6983	3420.7372	0.0000	1.0000
K2PI	37	-1670.9518	3420.9613	0.0000	1.0000
SYMG	41	-1666.4977	3421.2346	0.0000	1.0000
SYMIG	42	-1666.2831	3423.1215	0.0000	1.0000
SYMI	41	-1667.5707	3423.3806	0.0000	1.0000
GTR	43	-1670.6460	3434.1720	0.0000	1.0000
F81G	39	-1675.5771	3434.7859	0.0000	1.0000
F81IG	40	-1675.3684	3436.6680	0.0000	1.0000
F81I	39	-1676.6563	3436.9444	0.0000	1.0000
HKY	39	-1677.3706	3438.3729	0.0000	1.0000
JC69G	36	-1690.2233	3457.2294	0.0000	1.0000
JC69IG	37	-1690.0377	3459.1329	0.0000	1.0000
JC69I	36	-1691.2377	3459.2582	0.0000	1.0000
K2P	36	-1693.5977	3463.9782	0.0000	1.0000
SYM	40	-1689.5475	3465.0263	0.0000	1.0000
F81	38	-1698.1132	3477.5669	0.0000	1.0000
JC69	35	-1712.6688	3499.8536	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1646.6324	3381.2647	0.5380	0.5380
GTRIG	45	-1646.2825	3382.5650	0.2808	0.8188
GTRI	44	-1648.1876	3384.3753	0.1136	0.9324
HKYG	40	-1653.2933	3386.5865	0.0376	0.9699
HKYIG	41	-1652.9840	3387.9679	0.0188	0.9888
HKYI	40	-1654.5035	3389.0069	0.0112	1.0000
K2PG	37	-1669.9291	3413.8583	0.0000	1.0000
SYMG	41	-1666.4977	3414.9954	0.0000	1.0000
K2PIG	38	-1669.6983	3415.3967	0.0000	1.0000
K2PI	37	-1670.9518	3415.9037	0.0000	1.0000
SYMIG	42	-1666.2831	3416.5661	0.0000	1.0000
SYMI	41	-1667.5707	3417.1414	0.0000	1.0000
GTR	43	-1670.6460	3427.2920	0.0000	1.0000
F81G	39	-1675.5771	3429.1541	0.0000	1.0000
F81IG	40	-1675.3684	3430.7367	0.0000	1.0000
F81I	39	-1676.6563	3431.3127	0.0000	1.0000
HKY	39	-1677.3706	3432.7411	0.0000	1.0000
JC69G	36	-1690.2233	3452.4467	0.0000	1.0000
JC69IG	37	-1690.0377	3454.0754	0.0000	1.0000
JC69I	36	-1691.2377	3454.4755	0.0000	1.0000
SYM	40	-1689.5475	3459.0951	0.0000	1.0000
K2P	36	-1693.5977	3459.1954	0.0000	1.0000
F81	38	-1698.1132	3472.2264	0.0000	1.0000
JC69	35	-1712.6688	3495.3375	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1653.2933	3562.0617	0.7363	0.7363
HKYI	40	-1654.5035	3564.4821	0.2195	0.9559
HKYIG	41	-1652.9840	3567.8300	0.0412	0.9970
GTRG	44	-1646.6324	3574.2874	0.0016	0.9987
K2PG	37	-1669.9291	3576.1728	0.0006	0.9993
GTRI	44	-1648.1876	3577.3980	0.0003	0.9996
K2PI	37	-1670.9518	3578.2182	0.0002	0.9999
GTRIG	45	-1646.2825	3579.9746	0.0001	1.0000
K2PIG	38	-1669.6983	3582.0981	0.0000	1.0000
SYMG	41	-1666.4977	3594.8575	0.0000	1.0000
SYMI	41	-1667.5707	3597.0035	0.0000	1.0000
F81G	39	-1675.5771	3600.2424	0.0000	1.0000
SYMIG	42	-1666.2831	3600.8151	0.0000	1.0000
F81I	39	-1676.6563	3602.4010	0.0000	1.0000
HKY	39	-1677.3706	3603.8294	0.0000	1.0000
F81IG	40	-1675.3684	3606.2119	0.0000	1.0000
JC69G	36	-1690.2233	3610.3743	0.0000	1.0000
JC69I	36	-1691.2377	3612.4031	0.0000	1.0000
GTR	43	-1670.6460	3615.9278	0.0000	1.0000
JC69IG	37	-1690.0377	3616.3899	0.0000	1.0000
K2P	36	-1693.5977	3617.1231	0.0000	1.0000
SYM	40	-1689.5475	3634.5702	0.0000	1.0000
F81	38	-1698.1132	3638.9278	0.0000	1.0000
JC69	35	-1712.6688	3648.8783	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_362.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_362.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_362.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_362.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_362.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_362.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

