
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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/chr10_4435.phylip" (19 taxa, 504 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYIG


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	-1549.4253	3197.8899	0.5044	0.5044
GTRG	44	-1551.1931	3199.0136	0.2876	0.7920
HKYIG	41	-1555.3487	3200.1519	0.1628	0.9547
GTRI	44	-1553.2810	3203.1895	0.0356	0.9904
HKYG	40	-1559.4094	3205.9030	0.0092	0.9996
HKYI	40	-1562.4353	3211.9549	0.0004	1.0000
K2PIG	38	-1570.6429	3223.6600	0.0000	1.0000
SYMIG	42	-1566.4753	3224.7858	0.0000	1.0000
K2PG	37	-1574.8364	3229.7070	0.0000	1.0000
SYMG	41	-1571.2099	3231.8743	0.0000	1.0000
K2PI	37	-1577.7713	3235.5770	0.0000	1.0000
SYMI	41	-1573.9814	3237.4172	0.0000	1.0000
GTR	43	-1587.4902	3269.2065	0.0000	1.0000
HKY	39	-1593.9640	3272.6521	0.0000	1.0000
K2P	36	-1611.2744	3300.2533	0.0000	1.0000
SYM	40	-1607.2882	3301.6606	0.0000	1.0000
F81IG	40	-1615.6754	3318.4351	0.0000	1.0000
F81G	39	-1616.9306	3318.5853	0.0000	1.0000
F81I	39	-1619.5075	3323.7391	0.0000	1.0000
JC69IG	37	-1627.1728	3334.3800	0.0000	1.0000
JC69G	36	-1629.7286	3337.1617	0.0000	1.0000
JC69I	36	-1632.3345	3342.3735	0.0000	1.0000
F81	38	-1649.1814	3380.7371	0.0000	1.0000
JC69	35	-1663.0323	3401.4493	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1549.4253	3188.8506	0.5971	0.5971
GTRG	44	-1551.1931	3190.3861	0.2771	0.8741
HKYIG	41	-1555.3487	3192.6974	0.0872	0.9614
GTRI	44	-1553.2810	3194.5620	0.0343	0.9957
HKYG	40	-1559.4094	3198.8187	0.0041	0.9998
HKYI	40	-1562.4353	3204.8706	0.0002	1.0000
SYMIG	42	-1566.4753	3216.9507	0.0000	1.0000
K2PIG	38	-1570.6429	3217.2858	0.0000	1.0000
K2PG	37	-1574.8364	3223.6727	0.0000	1.0000
SYMG	41	-1571.2099	3224.4198	0.0000	1.0000
K2PI	37	-1577.7713	3229.5426	0.0000	1.0000
SYMI	41	-1573.9814	3229.9627	0.0000	1.0000
GTR	43	-1587.4902	3260.9804	0.0000	1.0000
HKY	39	-1593.9640	3265.9279	0.0000	1.0000
K2P	36	-1611.2744	3294.5488	0.0000	1.0000
SYM	40	-1607.2882	3294.5763	0.0000	1.0000
F81IG	40	-1615.6754	3311.3508	0.0000	1.0000
F81G	39	-1616.9306	3311.8611	0.0000	1.0000
F81I	39	-1619.5075	3317.0149	0.0000	1.0000
JC69IG	37	-1627.1728	3328.3456	0.0000	1.0000
JC69G	36	-1629.7286	3331.4572	0.0000	1.0000
JC69I	36	-1632.3345	3336.6690	0.0000	1.0000
F81	38	-1649.1814	3374.3629	0.0000	1.0000
JC69	35	-1663.0323	3396.0647	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-1555.3487	3365.8230	0.7057	0.7057
HKYG	40	-1559.4094	3367.7218	0.2731	0.9788
HKYI	40	-1562.4353	3373.7737	0.0132	0.9920
GTRG	44	-1551.1931	3376.1795	0.0040	0.9960
K2PIG	38	-1570.6429	3377.7437	0.0018	0.9978
GTRIG	45	-1549.4253	3378.8665	0.0010	0.9989
K2PG	37	-1574.8364	3379.9080	0.0006	0.9995
GTRI	44	-1553.2810	3380.3554	0.0005	1.0000
K2PI	37	-1577.7713	3385.7779	0.0000	1.0000
SYMIG	42	-1566.4753	3394.2989	0.0000	1.0000
SYMG	41	-1571.2099	3397.5454	0.0000	1.0000
SYMI	41	-1573.9814	3403.0883	0.0000	1.0000
HKY	39	-1593.9640	3430.6084	0.0000	1.0000
GTR	43	-1587.4902	3442.5512	0.0000	1.0000
K2P	36	-1611.2744	3446.5616	0.0000	1.0000
SYM	40	-1607.2882	3463.4794	0.0000	1.0000
F81G	39	-1616.9306	3476.5416	0.0000	1.0000
F81IG	40	-1615.6754	3480.2539	0.0000	1.0000
F81I	39	-1619.5075	3481.6954	0.0000	1.0000
JC69G	36	-1629.7286	3483.4700	0.0000	1.0000
JC69IG	37	-1627.1728	3484.5810	0.0000	1.0000
JC69I	36	-1632.3345	3488.6817	0.0000	1.0000
F81	38	-1649.1814	3534.8208	0.0000	1.0000
JC69	35	-1663.0323	3543.8548	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/chr10_4435.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4435.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/chr10_4435.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4435.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4435.phylip = 1 - 504;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_4435.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

