
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:10 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/chr1_5348.phylip" (19 taxa, 573 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1497.7397	3081.6448	0.2653	0.2653
HKYI	40	-1498.0132	3082.1918	0.2019	0.4672
GTRG	44	-1493.4116	3082.3232	0.1890	0.6562
GTRI	44	-1493.8152	3083.1304	0.1262	0.7825
HKYIG	41	-1497.3431	3083.1721	0.1236	0.9061
GTRIG	45	-1492.9335	3083.7228	0.0939	1.0000
HKY	39	-1518.2507	3120.3550	0.0000	1.0000
K2PG	37	-1520.7533	3120.7627	0.0000	1.0000
K2PI	37	-1520.9812	3121.2185	0.0000	1.0000
K2PIG	38	-1520.0948	3121.7403	0.0000	1.0000
GTR	43	-1514.9451	3123.0432	0.0000	1.0000
SYMG	41	-1519.7135	3127.9129	0.0000	1.0000
SYMI	41	-1519.9381	3128.3620	0.0000	1.0000
SYMIG	42	-1519.1019	3129.0188	0.0000	1.0000
K2P	36	-1540.1827	3157.3355	0.0000	1.0000
F81G	39	-1539.4209	3162.6954	0.0000	1.0000
F81I	39	-1539.5995	3163.0527	0.0000	1.0000
F81IG	40	-1539.2827	3164.7309	0.0000	1.0000
SYM	40	-1539.4039	3164.9733	0.0000	1.0000
JC69G	36	-1559.0179	3195.0059	0.0000	1.0000
JC69I	36	-1559.1846	3195.3394	0.0000	1.0000
JC69IG	37	-1558.8459	3196.9479	0.0000	1.0000
F81	38	-1558.2760	3198.1025	0.0000	1.0000
JC69	35	-1577.5669	3229.8266	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1493.4116	3074.8232	0.2549	0.2549
HKYG	40	-1497.7397	3075.4794	0.1836	0.4385
GTRI	44	-1493.8152	3075.6304	0.1702	0.6087
GTRIG	45	-1492.9335	3075.8670	0.1512	0.7599
HKYI	40	-1498.0132	3076.0264	0.1397	0.8996
HKYIG	41	-1497.3431	3076.6862	0.1004	1.0000
HKY	39	-1518.2507	3114.5013	0.0000	1.0000
K2PG	37	-1520.7533	3115.5066	0.0000	1.0000
GTR	43	-1514.9451	3115.8901	0.0000	1.0000
K2PI	37	-1520.9812	3115.9624	0.0000	1.0000
K2PIG	38	-1520.0948	3116.1897	0.0000	1.0000
SYMG	41	-1519.7135	3121.4270	0.0000	1.0000
SYMI	41	-1519.9381	3121.8762	0.0000	1.0000
SYMIG	42	-1519.1019	3122.2037	0.0000	1.0000
K2P	36	-1540.1827	3152.3654	0.0000	1.0000
F81G	39	-1539.4209	3156.8417	0.0000	1.0000
F81I	39	-1539.5995	3157.1991	0.0000	1.0000
F81IG	40	-1539.2827	3158.5655	0.0000	1.0000
SYM	40	-1539.4039	3158.8078	0.0000	1.0000
JC69G	36	-1559.0179	3190.0358	0.0000	1.0000
JC69I	36	-1559.1846	3190.3692	0.0000	1.0000
JC69IG	37	-1558.8459	3191.6918	0.0000	1.0000
F81	38	-1558.2760	3192.5520	0.0000	1.0000
JC69	35	-1577.5669	3225.1339	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1497.7397	3249.5148	0.5485	0.5485
HKYI	40	-1498.0132	3250.0618	0.4172	0.9657
HKYIG	41	-1497.3431	3255.0725	0.0341	0.9998
GTRG	44	-1493.4116	3266.2622	0.0001	0.9999
GTRI	44	-1493.8152	3267.0694	0.0001	1.0000
GTRIG	45	-1492.9335	3271.6569	0.0000	1.0000
K2PG	37	-1520.7533	3276.4894	0.0000	1.0000
K2PI	37	-1520.9812	3276.9452	0.0000	1.0000
K2PIG	38	-1520.0948	3281.5234	0.0000	1.0000
HKY	39	-1518.2507	3284.1859	0.0000	1.0000
SYMG	41	-1519.7135	3299.8133	0.0000	1.0000
SYMI	41	-1519.9381	3300.2625	0.0000	1.0000
GTR	43	-1514.9451	3302.9782	0.0000	1.0000
SYMIG	42	-1519.1019	3304.9409	0.0000	1.0000
K2P	36	-1540.1827	3308.9973	0.0000	1.0000
F81G	39	-1539.4209	3326.5263	0.0000	1.0000
F81I	39	-1539.5995	3326.8836	0.0000	1.0000
F81IG	40	-1539.2827	3332.6009	0.0000	1.0000
SYM	40	-1539.4039	3332.8433	0.0000	1.0000
JC69G	36	-1559.0179	3346.6677	0.0000	1.0000
JC69I	36	-1559.1846	3347.0011	0.0000	1.0000
JC69IG	37	-1558.8459	3352.6746	0.0000	1.0000
F81	38	-1558.2760	3357.8856	0.0000	1.0000
JC69	35	-1577.5669	3377.4149	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/chr1_5348.phylip = 1 - 573;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5348.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5348.phylip = 1 - 573;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5348.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;


[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/chr1_5348.phylip = 1 - 573;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5348.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

