
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:15 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/chr7_4965.phylip" (19 taxa, 519 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	-1484.2913	3064.9370	0.3142	0.3142
GTRIG	45	-1483.3550	3065.4626	0.2416	0.5559
HKYG	40	-1489.6841	3066.2300	0.1646	0.7205
HKYIG	41	-1488.6628	3066.5458	0.1406	0.8611
GTRI	44	-1485.5918	3067.5380	0.0856	0.9467
HKYI	40	-1490.8109	3068.4838	0.0533	1.0000
K2PG	37	-1504.7348	3089.3157	0.0000	1.0000
K2PIG	38	-1503.6954	3089.5658	0.0000	1.0000
K2PI	37	-1505.6209	3091.0880	0.0000	1.0000
SYMG	41	-1501.8801	3092.9804	0.0000	1.0000
SYMIG	42	-1500.9342	3093.4566	0.0000	1.0000
SYMI	41	-1502.7398	3094.6997	0.0000	1.0000
GTR	43	-1513.7209	3121.4080	0.0000	1.0000
HKY	39	-1519.1837	3122.8810	0.0000	1.0000
F81G	39	-1524.4670	3133.4477	0.0000	1.0000
F81IG	40	-1523.5427	3133.9473	0.0000	1.0000
F81I	39	-1525.5091	3135.5318	0.0000	1.0000
K2P	36	-1534.9035	3147.3340	0.0000	1.0000
SYM	40	-1531.7971	3150.4561	0.0000	1.0000
JC69G	36	-1537.9992	3153.5254	0.0000	1.0000
JC69IG	37	-1537.1858	3154.2177	0.0000	1.0000
JC69I	36	-1538.7808	3155.0886	0.0000	1.0000
F81	38	-1552.9636	3188.1023	0.0000	1.0000
JC69	35	-1566.6514	3208.5202	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1484.2913	3056.5825	0.3580	0.3580
GTRIG	45	-1483.3550	3056.7099	0.3359	0.6939
GTRI	44	-1485.5918	3059.1835	0.0975	0.7914
HKYIG	41	-1488.6628	3059.3256	0.0908	0.8823
HKYG	40	-1489.6841	3059.3681	0.0889	0.9712
HKYI	40	-1490.8109	3061.6219	0.0288	1.0000
K2PIG	38	-1503.6954	3083.3908	0.0000	1.0000
K2PG	37	-1504.7348	3083.4696	0.0000	1.0000
K2PI	37	-1505.6209	3085.2419	0.0000	1.0000
SYMG	41	-1501.8801	3085.7602	0.0000	1.0000
SYMIG	42	-1500.9342	3085.8684	0.0000	1.0000
SYMI	41	-1502.7398	3087.4796	0.0000	1.0000
GTR	43	-1513.7209	3113.4417	0.0000	1.0000
HKY	39	-1519.1837	3116.3675	0.0000	1.0000
F81G	39	-1524.4670	3126.9341	0.0000	1.0000
F81IG	40	-1523.5427	3127.0854	0.0000	1.0000
F81I	39	-1525.5091	3129.0182	0.0000	1.0000
K2P	36	-1534.9035	3141.8070	0.0000	1.0000
SYM	40	-1531.7971	3143.5942	0.0000	1.0000
JC69G	36	-1537.9992	3147.9985	0.0000	1.0000
JC69IG	37	-1537.1858	3148.3715	0.0000	1.0000
JC69I	36	-1538.7808	3149.5617	0.0000	1.0000
F81	38	-1552.9636	3181.9273	0.0000	1.0000
JC69	35	-1566.6514	3203.3028	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1489.6841	3229.4443	0.6885	0.6885
HKYI	40	-1490.8109	3231.6980	0.2231	0.9117
HKYIG	41	-1488.6628	3233.6537	0.0839	0.9956
K2PG	37	-1504.7348	3240.7900	0.0024	0.9980
K2PI	37	-1505.6209	3242.5623	0.0010	0.9989
GTRG	44	-1484.2913	3243.6663	0.0006	0.9995
K2PIG	38	-1503.6954	3244.9632	0.0003	0.9998
GTRI	44	-1485.5918	3246.2673	0.0002	0.9999
GTRIG	45	-1483.3550	3248.0456	0.0001	1.0000
SYMG	41	-1501.8801	3260.0883	0.0000	1.0000
SYMI	41	-1502.7398	3261.8076	0.0000	1.0000
SYMIG	42	-1500.9342	3264.4483	0.0000	1.0000
HKY	39	-1519.1837	3282.1917	0.0000	1.0000
F81G	39	-1524.4670	3292.7584	0.0000	1.0000
F81I	39	-1525.5091	3294.8425	0.0000	1.0000
K2P	36	-1534.9035	3294.8755	0.0000	1.0000
GTR	43	-1513.7209	3296.2736	0.0000	1.0000
F81IG	40	-1523.5427	3297.1616	0.0000	1.0000
JC69G	36	-1537.9992	3301.0670	0.0000	1.0000
JC69I	36	-1538.7808	3302.6302	0.0000	1.0000
JC69IG	37	-1537.1858	3305.6920	0.0000	1.0000
SYM	40	-1531.7971	3313.6704	0.0000	1.0000
F81	38	-1552.9636	3343.4996	0.0000	1.0000
JC69	35	-1566.6514	3352.1195	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/chr7_4965.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4965.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/chr7_4965.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4965.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/chr7_4965.phylip = 1 - 519;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4965.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

