
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:01 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/chr8_2614.phylip" (19 taxa, 889 characters)

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


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	-3078.6208	6252.1527	0.9936	0.9936
GTRG	44	-3084.7794	6262.2507	0.0064	1.0000
GTRI	44	-3090.8021	6274.2961	0.0000	1.0000
HKYIG	41	-3094.6668	6275.3997	0.0000	1.0000
HKYG	40	-3099.7663	6283.4006	0.0000	1.0000
SYMIG	42	-3097.6567	6283.5829	0.0000	1.0000
HKYI	40	-3104.3602	6292.5884	0.0000	1.0000
SYMG	41	-3104.0733	6294.2128	0.0000	1.0000
SYMI	41	-3108.9488	6303.9638	0.0000	1.0000
K2PIG	38	-3116.4566	6312.4002	0.0000	1.0000
K2PG	37	-3121.9401	6321.1845	0.0000	1.0000
K2PI	37	-3125.9662	6329.2367	0.0000	1.0000
F81IG	40	-3192.4530	6468.7740	0.0000	1.0000
F81G	39	-3197.0296	6475.7340	0.0000	1.0000
F81I	39	-3201.0810	6483.8370	0.0000	1.0000
JC69IG	37	-3210.7596	6498.8236	0.0000	1.0000
JC69G	36	-3216.6004	6508.3275	0.0000	1.0000
JC69I	36	-3220.4407	6516.0082	0.0000	1.0000
GTR	43	-3225.9765	6542.4312	0.0000	1.0000
HKY	39	-3243.1180	6567.9110	0.0000	1.0000
SYM	40	-3250.3112	6584.4903	0.0000	1.0000
K2P	36	-3268.6245	6612.3758	0.0000	1.0000
F81	38	-3337.4422	6754.3714	0.0000	1.0000
JC69	35	-3358.4834	6789.9211	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3078.6208	6247.2417	0.9943	0.9943
GTRG	44	-3084.7794	6257.5588	0.0057	1.0000
GTRI	44	-3090.8021	6269.6042	0.0000	1.0000
HKYIG	41	-3094.6668	6271.3336	0.0000	1.0000
SYMIG	42	-3097.6567	6279.3134	0.0000	1.0000
HKYG	40	-3099.7663	6279.5327	0.0000	1.0000
HKYI	40	-3104.3602	6288.7205	0.0000	1.0000
SYMG	41	-3104.0733	6290.1466	0.0000	1.0000
SYMI	41	-3108.9488	6299.8977	0.0000	1.0000
K2PIG	38	-3116.4566	6308.9132	0.0000	1.0000
K2PG	37	-3121.9401	6317.8802	0.0000	1.0000
K2PI	37	-3125.9662	6325.9324	0.0000	1.0000
F81IG	40	-3192.4530	6464.9061	0.0000	1.0000
F81G	39	-3197.0296	6472.0591	0.0000	1.0000
F81I	39	-3201.0810	6480.1620	0.0000	1.0000
JC69IG	37	-3210.7596	6495.5192	0.0000	1.0000
JC69G	36	-3216.6004	6505.2007	0.0000	1.0000
JC69I	36	-3220.4407	6512.8815	0.0000	1.0000
GTR	43	-3225.9765	6537.9531	0.0000	1.0000
HKY	39	-3243.1180	6564.2360	0.0000	1.0000
SYM	40	-3250.3112	6580.6223	0.0000	1.0000
K2P	36	-3268.6245	6609.2491	0.0000	1.0000
F81	38	-3337.4422	6750.8843	0.0000	1.0000
JC69	35	-3358.4834	6786.9668	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRIG	45	-3078.6208	6462.7960	0.8592	0.8592
HKYIG	41	-3094.6668	6467.7275	0.0730	0.9321
GTRG	44	-3084.7794	6468.3231	0.0542	0.9863
HKYG	40	-3099.7663	6471.1366	0.0133	0.9996
HKYI	40	-3104.3602	6480.3244	0.0001	0.9997
GTRI	44	-3090.8021	6480.3684	0.0001	0.9999
SYMIG	42	-3097.6567	6480.4975	0.0001	1.0000
SYMG	41	-3104.0733	6486.5406	0.0000	1.0000
K2PIG	38	-3116.4566	6490.9369	0.0000	1.0000
K2PG	37	-3121.9401	6495.1138	0.0000	1.0000
SYMI	41	-3108.9488	6496.2916	0.0000	1.0000
K2PI	37	-3125.9662	6503.1660	0.0000	1.0000
F81IG	40	-3192.4530	6656.5099	0.0000	1.0000
F81G	39	-3197.0296	6658.8729	0.0000	1.0000
F81I	39	-3201.0810	6666.9758	0.0000	1.0000
JC69IG	37	-3210.7596	6672.7528	0.0000	1.0000
JC69G	36	-3216.6004	6677.6442	0.0000	1.0000
JC69I	36	-3220.4407	6685.3250	0.0000	1.0000
GTR	43	-3225.9765	6743.9273	0.0000	1.0000
HKY	39	-3243.1180	6751.0498	0.0000	1.0000
SYM	40	-3250.3112	6772.2262	0.0000	1.0000
K2P	36	-3268.6245	6781.6926	0.0000	1.0000
F81	38	-3337.4422	6932.9080	0.0000	1.0000
JC69	35	-3358.4834	6954.6202	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/chr8_2614.phylip = 1 - 889;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2614.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/chr8_2614.phylip = 1 - 889;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2614.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 (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2614.phylip = 1 - 889;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_2614.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;


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End of Output

