
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:06 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_28694.phylip" (19 taxa, 468 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1493.2981	3074.2777	0.2588	0.2588
GTRG	44	-1488.5807	3074.5230	0.2289	0.4876
HKYI	40	-1493.6264	3074.9343	0.1863	0.6740
GTRI	44	-1489.0344	3075.4304	0.1454	0.8194
HKYIG	41	-1493.1130	3076.3106	0.0936	0.9130
GTRIG	45	-1488.4091	3076.6287	0.0799	0.9929
K2PG	37	-1501.3968	3083.3332	0.0028	0.9957
K2PI	37	-1501.6743	3083.8881	0.0021	0.9978
K2PIG	38	-1501.2110	3085.3310	0.0010	0.9989
SYMG	41	-1498.2718	3086.6282	0.0005	0.9994
SYMI	41	-1498.5789	3087.2422	0.0004	0.9998
SYMIG	42	-1498.0998	3088.6984	0.0002	1.0000
HKY	39	-1504.1616	3093.6130	0.0000	1.0000
GTR	43	-1500.0980	3095.1205	0.0000	1.0000
K2P	36	-1512.0170	3102.2149	0.0000	1.0000
SYM	40	-1509.0552	3105.7919	0.0000	1.0000
F81G	39	-1526.1857	3137.6612	0.0000	1.0000
F81I	39	-1526.4284	3138.1466	0.0000	1.0000
F81IG	40	-1526.0210	3139.7235	0.0000	1.0000
JC69G	36	-1532.6314	3143.4437	0.0000	1.0000
JC69I	36	-1532.8386	3143.8581	0.0000	1.0000
JC69IG	37	-1532.4680	3145.4755	0.0000	1.0000
F81	38	-1536.1863	3155.2816	0.0000	1.0000
JC69	35	-1542.5456	3160.9246	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1488.5807	3065.1613	0.3188	0.3188
GTRI	44	-1489.0344	3066.0687	0.2025	0.5213
HKYG	40	-1493.2981	3066.5962	0.1556	0.6769
GTRIG	45	-1488.4091	3066.8182	0.1392	0.8161
HKYI	40	-1493.6264	3067.2528	0.1120	0.9282
HKYIG	41	-1493.1130	3068.2261	0.0689	0.9970
K2PG	37	-1501.3968	3076.7937	0.0009	0.9980
K2PI	37	-1501.6743	3077.3486	0.0007	0.9987
K2PIG	38	-1501.2110	3078.4219	0.0004	0.9991
SYMG	41	-1498.2718	3078.5437	0.0004	0.9995
SYMI	41	-1498.5789	3079.1577	0.0003	0.9998
SYMIG	42	-1498.0998	3080.1996	0.0002	1.0000
GTR	43	-1500.0980	3086.1959	0.0000	1.0000
HKY	39	-1504.1616	3086.3232	0.0000	1.0000
K2P	36	-1512.0170	3096.0340	0.0000	1.0000
SYM	40	-1509.0552	3098.1104	0.0000	1.0000
F81G	39	-1526.1857	3130.3714	0.0000	1.0000
F81I	39	-1526.4284	3130.8569	0.0000	1.0000
F81IG	40	-1526.0210	3132.0420	0.0000	1.0000
JC69G	36	-1532.6314	3137.2627	0.0000	1.0000
JC69I	36	-1532.8386	3137.6771	0.0000	1.0000
JC69IG	37	-1532.4680	3138.9359	0.0000	1.0000
F81	38	-1536.1863	3148.3725	0.0000	1.0000
JC69	35	-1542.5456	3155.0912	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1501.3968	3230.2870	0.4181	0.4181
K2PI	37	-1501.6743	3230.8419	0.3168	0.7350
HKYG	40	-1493.2981	3232.5350	0.1359	0.8708
HKYI	40	-1493.6264	3233.1916	0.0979	0.9687
K2PIG	38	-1501.2110	3236.0637	0.0233	0.9920
HKYIG	41	-1493.1130	3238.3133	0.0076	0.9995
K2P	36	-1512.0170	3245.3788	0.0002	0.9997
GTRG	44	-1488.5807	3247.6939	0.0001	0.9998
HKY	39	-1504.1616	3248.1135	0.0001	0.9999
GTRI	44	-1489.0344	3248.6013	0.0000	0.9999
SYMG	41	-1498.2718	3248.6309	0.0000	1.0000
SYMI	41	-1498.5789	3249.2449	0.0000	1.0000
GTRIG	45	-1488.4091	3253.4993	0.0000	1.0000
SYMIG	42	-1498.0998	3254.4352	0.0000	1.0000
SYM	40	-1509.0552	3264.0492	0.0000	1.0000
GTR	43	-1500.0980	3264.5801	0.0000	1.0000
JC69G	36	-1532.6314	3286.6076	0.0000	1.0000
JC69I	36	-1532.8386	3287.0220	0.0000	1.0000
F81G	39	-1526.1857	3292.1617	0.0000	1.0000
JC69IG	37	-1532.4680	3292.4293	0.0000	1.0000
F81I	39	-1526.4284	3292.6471	0.0000	1.0000
F81IG	40	-1526.0210	3297.9808	0.0000	1.0000
JC69	35	-1542.5456	3300.2876	0.0000	1.0000
F81	38	-1536.1863	3306.0143	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_28694.phylip = 1 - 468;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28694.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_28694.phylip = 1 - 468;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28694.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28694.phylip = 1 - 468;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28694.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

