
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:10 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/chr2_8651.phylip" (19 taxa, 590 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: K2PG


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	-3393.5306	6884.6715	0.8123	0.8123
GTRG	44	-3396.4265	6888.1190	0.1449	0.9572
SYMIG	42	-3400.2678	6891.1388	0.0320	0.9893
SYMG	41	-3403.1023	6894.4893	0.0060	0.9953
GTRI	44	-3400.0392	6895.3444	0.0039	0.9992
HKYIG	41	-3405.8085	6899.9016	0.0004	0.9996
HKYG	40	-3407.9508	6901.8761	0.0001	0.9997
K2PIG	38	-3410.4492	6902.2777	0.0001	0.9998
SYMI	41	-3407.2204	6902.7254	0.0001	0.9999
K2PG	37	-3412.2797	6903.6536	0.0001	1.0000
HKYI	40	-3413.5234	6913.0213	0.0000	1.0000
K2PI	37	-3418.0170	6915.1283	0.0000	1.0000
JC69G	36	-3495.5538	7067.9250	0.0000	1.0000
F81G	39	-3492.3855	7068.4438	0.0000	1.0000
JC69IG	37	-3497.4519	7073.9980	0.0000	1.0000
F81IG	40	-3494.1581	7074.2906	0.0000	1.0000
GTR	43	-3493.2906	7079.5117	0.0000	1.0000
F81I	39	-3498.6883	7081.0494	0.0000	1.0000
JC69I	36	-3502.1234	7081.0642	0.0000	1.0000
SYM	40	-3502.8309	7091.6363	0.0000	1.0000
HKY	39	-3507.7449	7099.1625	0.0000	1.0000
K2P	36	-3514.3881	7105.5936	0.0000	1.0000
F81	38	-3588.5888	7258.5568	0.0000	1.0000
JC69	35	-3592.7303	7260.0093	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3393.5306	6877.0612	0.8458	0.8458
GTRG	44	-3396.4265	6880.8530	0.1270	0.9728
SYMIG	42	-3400.2678	6884.5355	0.0201	0.9930
GTRI	44	-3400.0392	6888.0784	0.0034	0.9964
SYMG	41	-3403.1023	6888.2046	0.0032	0.9996
HKYIG	41	-3405.8085	6893.6169	0.0002	0.9998
HKYG	40	-3407.9508	6895.9016	0.0001	0.9999
SYMI	41	-3407.2204	6896.4407	0.0001	0.9999
K2PIG	38	-3410.4492	6896.8984	0.0000	1.0000
K2PG	37	-3412.2797	6898.5594	0.0000	1.0000
HKYI	40	-3413.5234	6907.0468	0.0000	1.0000
K2PI	37	-3418.0170	6910.0341	0.0000	1.0000
F81G	39	-3492.3855	7062.7711	0.0000	1.0000
JC69G	36	-3495.5538	7063.1076	0.0000	1.0000
F81IG	40	-3494.1581	7068.3161	0.0000	1.0000
JC69IG	37	-3497.4519	7068.9038	0.0000	1.0000
GTR	43	-3493.2906	7072.5813	0.0000	1.0000
F81I	39	-3498.6883	7075.3766	0.0000	1.0000
JC69I	36	-3502.1234	7076.2469	0.0000	1.0000
SYM	40	-3502.8309	7085.6618	0.0000	1.0000
HKY	39	-3507.7449	7093.4898	0.0000	1.0000
K2P	36	-3514.3881	7100.7762	0.0000	1.0000
F81	38	-3588.5888	7253.1775	0.0000	1.0000
JC69	35	-3592.7303	7255.4605	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3412.2797	7060.6240	0.7589	0.7589
K2PIG	38	-3410.4492	7063.3430	0.1949	0.9538
SYMG	41	-3403.1023	7067.7896	0.0211	0.9749
SYMIG	42	-3400.2678	7068.5007	0.0148	0.9897
HKYG	40	-3407.9508	7071.1065	0.0040	0.9937
K2PI	37	-3418.0170	7072.0986	0.0024	0.9962
HKYIG	41	-3405.8085	7073.2020	0.0014	0.9976
GTRG	44	-3396.4265	7073.5784	0.0012	0.9987
GTRIG	45	-3393.5306	7074.1667	0.0009	0.9996
SYMI	41	-3407.2204	7076.0257	0.0003	1.0000
GTRI	44	-3400.0392	7080.8038	0.0000	1.0000
HKYI	40	-3413.5234	7082.2517	0.0000	1.0000
JC69G	36	-3495.5538	7220.7921	0.0000	1.0000
JC69IG	37	-3497.4519	7230.9683	0.0000	1.0000
F81G	39	-3492.3855	7233.5958	0.0000	1.0000
JC69I	36	-3502.1234	7233.9313	0.0000	1.0000
F81IG	40	-3494.1581	7243.5210	0.0000	1.0000
F81I	39	-3498.6883	7246.2014	0.0000	1.0000
K2P	36	-3514.3881	7258.4607	0.0000	1.0000
SYM	40	-3502.8309	7260.8667	0.0000	1.0000
GTR	43	-3493.2906	7260.9265	0.0000	1.0000
HKY	39	-3507.7449	7264.3146	0.0000	1.0000
JC69	35	-3592.7303	7408.7648	0.0000	1.0000
F81	38	-3588.5888	7419.6222	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/chr2_8651.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8651.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/chr2_8651.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8651.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8651.phylip = 1 - 590;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8651.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

