
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:18 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/chr5_10906.phylip" (19 taxa, 751 characters)

Minimum AIC  model: GTRIG
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	-1495.9258	3076.4713	0.2419	0.2419
GTRI	44	-1491.4921	3076.5933	0.2276	0.4695
GTRIG	45	-1490.4647	3076.8017	0.2051	0.6745
HKYIG	41	-1495.2046	3077.2667	0.1625	0.8371
HKYI	40	-1496.4728	3077.5654	0.1400	0.9770
GTRG	44	-1493.8255	3081.2600	0.0221	0.9991
F81IG	40	-1502.2700	3089.1596	0.0004	0.9995
F81I	39	-1503.4117	3089.2116	0.0004	0.9999
F81G	39	-1505.4323	3093.2527	0.0001	1.0000
SYMI	41	-1508.3732	3103.6039	0.0000	1.0000
SYMIG	42	-1507.4056	3103.9129	0.0000	1.0000
K2PIG	38	-1511.9243	3104.0116	0.0000	1.0000
K2PI	37	-1513.1025	3104.1489	0.0000	1.0000
SYMG	41	-1510.4230	3107.7035	0.0000	1.0000
K2PG	37	-1515.0871	3108.1180	0.0000	1.0000
HKY	39	-1512.9408	3108.2698	0.0000	1.0000
GTR	43	-1511.1696	3113.6914	0.0000	1.0000
JC69I	36	-1519.2479	3114.2269	0.0000	1.0000
JC69IG	37	-1518.1463	3114.2365	0.0000	1.0000
JC69G	36	-1521.1700	3118.0711	0.0000	1.0000
F81	38	-1522.2932	3124.7494	0.0000	1.0000
SYM	40	-1527.3736	3139.3668	0.0000	1.0000
K2P	36	-1531.8825	3139.4962	0.0000	1.0000
JC69	35	-1537.8875	3149.2994	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1490.4647	3070.9294	0.2823	0.2823
GTRI	44	-1491.4921	3070.9842	0.2747	0.5570
HKYG	40	-1495.9258	3071.8516	0.1780	0.7350
HKYIG	41	-1495.2046	3072.4091	0.1347	0.8697
HKYI	40	-1496.4728	3072.9457	0.1030	0.9727
GTRG	44	-1493.8255	3075.6509	0.0266	0.9994
F81IG	40	-1502.2700	3084.5399	0.0003	0.9997
F81I	39	-1503.4117	3084.8234	0.0003	1.0000
F81G	39	-1505.4323	3088.8645	0.0000	1.0000
SYMI	41	-1508.3732	3098.7464	0.0000	1.0000
SYMIG	42	-1507.4056	3098.8112	0.0000	1.0000
K2PIG	38	-1511.9243	3099.8486	0.0000	1.0000
K2PI	37	-1513.1025	3100.2050	0.0000	1.0000
SYMG	41	-1510.4230	3102.8460	0.0000	1.0000
HKY	39	-1512.9408	3103.8816	0.0000	1.0000
K2PG	37	-1515.0871	3104.1741	0.0000	1.0000
GTR	43	-1511.1696	3108.3392	0.0000	1.0000
JC69IG	37	-1518.1463	3110.2926	0.0000	1.0000
JC69I	36	-1519.2479	3110.4958	0.0000	1.0000
JC69G	36	-1521.1700	3114.3400	0.0000	1.0000
F81	38	-1522.2932	3120.5864	0.0000	1.0000
SYM	40	-1527.3736	3134.7471	0.0000	1.0000
K2P	36	-1531.8825	3135.7651	0.0000	1.0000
JC69	35	-1537.8875	3145.7749	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1495.9258	3256.7078	0.5974	0.5974
HKYI	40	-1496.4728	3257.8019	0.3457	0.9430
HKYIG	41	-1495.2046	3261.8868	0.0448	0.9879
F81I	39	-1503.4117	3265.0583	0.0092	0.9971
F81G	39	-1505.4323	3269.0993	0.0012	0.9983
F81IG	40	-1502.2700	3269.3961	0.0010	0.9993
K2PI	37	-1513.1025	3271.1970	0.0004	0.9998
GTRI	44	-1491.4921	3274.3261	0.0001	0.9998
K2PG	37	-1515.0871	3275.1661	0.0001	0.9999
K2PIG	38	-1511.9243	3275.4621	0.0001	1.0000
JC69I	36	-1519.2479	3276.8664	0.0000	1.0000
GTRIG	45	-1490.4647	3278.8926	0.0000	1.0000
GTRG	44	-1493.8255	3278.9928	0.0000	1.0000
JC69G	36	-1521.1700	3280.7106	0.0000	1.0000
JC69IG	37	-1518.1463	3281.2846	0.0000	1.0000
HKY	39	-1512.9408	3284.1164	0.0000	1.0000
SYMI	41	-1508.3732	3288.2240	0.0000	1.0000
SYMG	41	-1510.4230	3292.3236	0.0000	1.0000
SYMIG	42	-1507.4056	3292.9103	0.0000	1.0000
F81	38	-1522.2932	3296.1999	0.0000	1.0000
K2P	36	-1531.8825	3302.1357	0.0000	1.0000
GTR	43	-1511.1696	3307.0596	0.0000	1.0000
JC69	35	-1537.8875	3307.5241	0.0000	1.0000
SYM	40	-1527.3736	3319.6033	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/chr5_10906.phylip = 1 - 751;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10906.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10906.phylip = 1 - 751;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10906.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/chr5_10906.phylip = 1 - 751;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10906.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

