
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:14 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/chr11_1999.phylip" (19 taxa, 742 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-3300.9487	6695.5789	0.9779	0.9779
GTRIG	45	-3303.6111	6703.1704	0.0220	0.9999
GTRI	44	-3310.3294	6714.3403	0.0001	1.0000
HKYG	40	-3320.8511	6726.3811	0.0000	1.0000
HKYIG	41	-3320.0845	6727.0889	0.0000	1.0000
HKYI	40	-3325.6902	6736.0595	0.0000	1.0000
K2PG	37	-3337.1384	6752.2711	0.0000	1.0000
K2PI	37	-3340.0060	6758.0063	0.0000	1.0000
SYMG	41	-3337.7804	6762.4809	0.0000	1.0000
SYMIG	42	-3336.8456	6762.8586	0.0000	1.0000
K2PIG	38	-3342.8277	6765.8717	0.0000	1.0000
SYMI	41	-3340.2263	6767.3726	0.0000	1.0000
F81G	39	-3388.3025	6859.0494	0.0000	1.0000
F81IG	40	-3387.4157	6859.5104	0.0000	1.0000
F81I	39	-3391.5221	6865.4886	0.0000	1.0000
JC69IG	37	-3401.0587	6880.1117	0.0000	1.0000
JC69G	36	-3402.4649	6880.7085	0.0000	1.0000
JC69I	36	-3404.5577	6884.8941	0.0000	1.0000
GTR	43	-3412.3131	6916.0474	0.0000	1.0000
HKY	39	-3423.1588	6928.7621	0.0000	1.0000
SYM	40	-3434.1126	6952.9041	0.0000	1.0000
K2P	36	-3439.5894	6954.9576	0.0000	1.0000
F81	38	-3482.1274	7044.4710	0.0000	1.0000
JC69	35	-3494.4960	7062.5613	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3300.9487	6689.8974	0.9749	0.9749
GTRIG	45	-3303.6111	6697.2221	0.0250	0.9999
GTRI	44	-3310.3294	6708.6588	0.0001	1.0000
HKYG	40	-3320.8511	6721.7021	0.0000	1.0000
HKYIG	41	-3320.0845	6722.1689	0.0000	1.0000
HKYI	40	-3325.6902	6731.3805	0.0000	1.0000
K2PG	37	-3337.1384	6748.2768	0.0000	1.0000
K2PI	37	-3340.0060	6754.0120	0.0000	1.0000
SYMG	41	-3337.7804	6757.5609	0.0000	1.0000
SYMIG	42	-3336.8456	6757.6912	0.0000	1.0000
K2PIG	38	-3342.8277	6761.6555	0.0000	1.0000
SYMI	41	-3340.2263	6762.4526	0.0000	1.0000
F81G	39	-3388.3025	6854.6050	0.0000	1.0000
F81IG	40	-3387.4157	6854.8314	0.0000	1.0000
F81I	39	-3391.5221	6861.0442	0.0000	1.0000
JC69IG	37	-3401.0587	6876.1174	0.0000	1.0000
JC69G	36	-3402.4649	6876.9297	0.0000	1.0000
JC69I	36	-3404.5577	6881.1154	0.0000	1.0000
GTR	43	-3412.3131	6910.6262	0.0000	1.0000
HKY	39	-3423.1588	6924.3177	0.0000	1.0000
SYM	40	-3434.1126	6948.2251	0.0000	1.0000
K2P	36	-3439.5894	6951.1788	0.0000	1.0000
F81	38	-3482.1274	7040.2548	0.0000	1.0000
JC69	35	-3494.4960	7058.9919	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3300.9487	6892.7088	0.9960	0.9960
GTRIG	45	-3303.6111	6904.6429	0.0026	0.9986
HKYG	40	-3320.8511	6906.0761	0.0012	0.9998
HKYIG	41	-3320.0845	6911.1523	0.0001	0.9999
GTRI	44	-3310.3294	6911.4701	0.0001	1.0000
HKYI	40	-3325.6902	6915.7544	0.0000	1.0000
K2PG	37	-3337.1384	6918.8227	0.0000	1.0000
K2PI	37	-3340.0060	6924.5579	0.0000	1.0000
K2PIG	38	-3342.8277	6936.8108	0.0000	1.0000
SYMG	41	-3337.7804	6946.5442	0.0000	1.0000
SYMIG	42	-3336.8456	6951.2839	0.0000	1.0000
SYMI	41	-3340.2263	6951.4360	0.0000	1.0000
F81G	39	-3388.3025	7034.3696	0.0000	1.0000
F81IG	40	-3387.4157	7039.2053	0.0000	1.0000
F81I	39	-3391.5221	7040.8088	0.0000	1.0000
JC69G	36	-3402.4649	7042.8663	0.0000	1.0000
JC69IG	37	-3401.0587	7046.6633	0.0000	1.0000
JC69I	36	-3404.5577	7047.0520	0.0000	1.0000
HKY	39	-3423.1588	7104.0823	0.0000	1.0000
GTR	43	-3412.3131	7108.8282	0.0000	1.0000
K2P	36	-3439.5894	7117.1154	0.0000	1.0000
SYM	40	-3434.1126	7132.5991	0.0000	1.0000
F81	38	-3482.1274	7215.4101	0.0000	1.0000
JC69	35	-3494.4960	7220.3192	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/chr11_1999.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1999.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/chr11_1999.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1999.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1999.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1999.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;


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End of Output

