
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:30 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/chr12_5897.phylip" (19 taxa, 403 characters)

Minimum AIC  model: HKYG
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	-1489.8738	3068.8083	0.6186	0.6186
HKYIG	41	-1489.7939	3071.1279	0.1940	0.8125
HKYI	40	-1491.6441	3072.3490	0.1053	0.9179
GTRG	44	-1487.4949	3074.0512	0.0450	0.9628
GTRIG	45	-1487.4041	3076.4049	0.0139	0.9767
K2PG	37	-1497.7659	3077.2359	0.0091	0.9858
GTRI	44	-1489.1075	3077.2765	0.0090	0.9948
K2PIG	38	-1497.6993	3079.5415	0.0029	0.9977
K2PI	37	-1499.4383	3080.5808	0.0017	0.9994
SYMG	41	-1495.9812	3083.5026	0.0004	0.9998
SYMIG	42	-1495.9146	3085.8626	0.0001	0.9999
SYMI	41	-1497.6211	3086.7823	0.0001	1.0000
HKY	39	-1509.2497	3105.0944	0.0000	1.0000
GTR	43	-1507.6007	3111.7418	0.0000	1.0000
K2P	36	-1516.7678	3112.8143	0.0000	1.0000
SYM	40	-1515.2914	3119.6435	0.0000	1.0000
F81G	39	-1528.6261	3143.8473	0.0000	1.0000
F81IG	40	-1528.5165	3146.0938	0.0000	1.0000
F81I	39	-1530.7010	3147.9971	0.0000	1.0000
JC69G	36	-1535.9399	3151.1584	0.0000	1.0000
JC69IG	37	-1535.8317	3153.3675	0.0000	1.0000
JC69I	36	-1538.0468	3155.3724	0.0000	1.0000
F81	38	-1547.9505	3180.0439	0.0000	1.0000
JC69	35	-1552.4029	3181.6723	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1489.8738	3059.7476	0.5267	0.5267
HKYIG	41	-1489.7939	3061.5877	0.2099	0.7366
GTRG	44	-1487.4949	3062.9898	0.1041	0.8407
HKYI	40	-1491.6441	3063.2882	0.0897	0.9304
GTRIG	45	-1487.4041	3064.8082	0.0419	0.9723
GTRI	44	-1489.1075	3066.2151	0.0208	0.9931
K2PG	37	-1497.7659	3069.5318	0.0040	0.9970
K2PIG	38	-1497.6993	3071.3987	0.0016	0.9986
K2PI	37	-1499.4383	3072.8767	0.0007	0.9993
SYMG	41	-1495.9812	3073.9624	0.0004	0.9997
SYMIG	42	-1495.9146	3075.8293	0.0002	0.9999
SYMI	41	-1497.6211	3077.2422	0.0001	1.0000
HKY	39	-1509.2497	3096.4993	0.0000	1.0000
GTR	43	-1507.6007	3101.2014	0.0000	1.0000
K2P	36	-1516.7678	3105.5357	0.0000	1.0000
SYM	40	-1515.2914	3110.5827	0.0000	1.0000
F81G	39	-1528.6261	3135.2522	0.0000	1.0000
F81IG	40	-1528.5165	3137.0330	0.0000	1.0000
F81I	39	-1530.7010	3139.4021	0.0000	1.0000
JC69G	36	-1535.9399	3143.8797	0.0000	1.0000
JC69IG	37	-1535.8317	3145.6634	0.0000	1.0000
JC69I	36	-1538.0468	3148.0937	0.0000	1.0000
F81	38	-1547.9505	3171.9010	0.0000	1.0000
JC69	35	-1552.4029	3174.8058	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1497.7659	3217.4925	0.6075	0.6075
HKYG	40	-1489.8738	3219.7050	0.2010	0.8085
K2PI	37	-1499.4383	3220.8373	0.1141	0.9225
HKYI	40	-1491.6441	3223.2457	0.0342	0.9568
K2PIG	38	-1497.6993	3223.3582	0.0323	0.9891
HKYIG	41	-1489.7939	3225.5441	0.0108	1.0000
SYMG	41	-1495.9812	3237.9188	0.0000	1.0000
GTRG	44	-1487.4949	3238.9430	0.0000	1.0000
SYMI	41	-1497.6211	3241.1986	0.0000	1.0000
GTRI	44	-1489.1075	3242.1683	0.0000	1.0000
SYMIG	42	-1495.9146	3243.7846	0.0000	1.0000
GTRIG	45	-1487.4041	3244.7604	0.0000	1.0000
K2P	36	-1516.7678	3249.4974	0.0000	1.0000
HKY	39	-1509.2497	3252.4579	0.0000	1.0000
SYM	40	-1515.2914	3270.5402	0.0000	1.0000
GTR	43	-1507.6007	3273.1557	0.0000	1.0000
JC69G	36	-1535.9399	3287.8415	0.0000	1.0000
F81G	39	-1528.6261	3291.2107	0.0000	1.0000
JC69I	36	-1538.0468	3292.0554	0.0000	1.0000
JC69IG	37	-1535.8317	3293.6240	0.0000	1.0000
F81I	39	-1530.7010	3295.3606	0.0000	1.0000
F81IG	40	-1528.5165	3296.9904	0.0000	1.0000
JC69	35	-1552.4029	3314.7686	0.0000	1.0000
F81	38	-1547.9505	3323.8606	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5897.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5897.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5897.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5897.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/chr12_5897.phylip = 1 - 403;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5897.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

