
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:02 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_5281.phylip" (19 taxa, 677 characters)

Minimum AIC  model: HKYG
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	-1481.7978	3048.7529	0.3617	0.3617
HKYI	40	-1481.8639	3048.8850	0.3386	0.7004
HKYIG	41	-1481.1028	3049.6292	0.2334	0.9338
GTRG	44	-1479.8784	3054.0227	0.0259	0.9597
GTRI	44	-1479.9605	3054.1867	0.0239	0.9836
GTRIG	45	-1479.1903	3054.9416	0.0164	1.0000
HKY	39	-1495.3804	3073.6588	0.0000	1.0000
K2PG	37	-1498.7966	3075.9938	0.0000	1.0000
K2PI	37	-1498.8055	3076.0115	0.0000	1.0000
K2PIG	38	-1498.1637	3076.9731	0.0000	1.0000
GTR	43	-1493.4405	3078.8588	0.0000	1.0000
SYMG	41	-1497.9202	3083.2640	0.0000	1.0000
SYMI	41	-1497.9515	3083.3266	0.0000	1.0000
SYMIG	42	-1497.2830	3084.2631	0.0000	1.0000
F81G	39	-1502.8975	3088.6930	0.0000	1.0000
F81I	39	-1502.9282	3088.7543	0.0000	1.0000
F81IG	40	-1502.3046	3089.7663	0.0000	1.0000
K2P	36	-1512.7616	3101.6857	0.0000	1.0000
SYM	40	-1511.6016	3108.3605	0.0000	1.0000
F81	38	-1516.5938	3113.8333	0.0000	1.0000
JC69G	36	-1519.4709	3115.1042	0.0000	1.0000
JC69I	36	-1519.4910	3115.1444	0.0000	1.0000
JC69IG	37	-1518.9182	3116.2371	0.0000	1.0000
JC69	35	-1533.2207	3140.3728	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1481.7978	3043.5957	0.3328	0.3328
HKYI	40	-1481.8639	3043.7278	0.3116	0.6444
HKYIG	41	-1481.1028	3044.2056	0.2453	0.8897
GTRG	44	-1479.8784	3047.7569	0.0416	0.9313
GTRI	44	-1479.9605	3047.9209	0.0383	0.9696
GTRIG	45	-1479.1903	3048.3806	0.0304	1.0000
HKY	39	-1495.3804	3068.7609	0.0000	1.0000
K2PG	37	-1498.7966	3071.5932	0.0000	1.0000
K2PI	37	-1498.8055	3071.6109	0.0000	1.0000
K2PIG	38	-1498.1637	3072.3273	0.0000	1.0000
GTR	43	-1493.4405	3072.8809	0.0000	1.0000
SYMG	41	-1497.9202	3077.8404	0.0000	1.0000
SYMI	41	-1497.9515	3077.9030	0.0000	1.0000
SYMIG	42	-1497.2830	3078.5659	0.0000	1.0000
F81G	39	-1502.8975	3083.7951	0.0000	1.0000
F81I	39	-1502.9282	3083.8563	0.0000	1.0000
F81IG	40	-1502.3046	3084.6091	0.0000	1.0000
K2P	36	-1512.7616	3097.5232	0.0000	1.0000
SYM	40	-1511.6016	3103.2033	0.0000	1.0000
F81	38	-1516.5938	3109.1875	0.0000	1.0000
JC69G	36	-1519.4709	3110.9417	0.0000	1.0000
JC69I	36	-1519.4910	3110.9819	0.0000	1.0000
JC69IG	37	-1518.9182	3111.8365	0.0000	1.0000
JC69	35	-1533.2207	3136.4415	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1481.7978	3224.3025	0.4964	0.4964
HKYI	40	-1481.8639	3224.4346	0.4646	0.9610
HKYIG	41	-1481.1028	3229.4301	0.0382	0.9992
K2PG	37	-1498.7966	3238.7470	0.0004	0.9996
K2PI	37	-1498.8055	3238.7647	0.0004	0.9999
K2PIG	38	-1498.1637	3243.9988	0.0000	1.0000
HKY	39	-1495.3804	3244.9501	0.0000	1.0000
GTRG	44	-1479.8784	3246.5344	0.0000	1.0000
GTRI	44	-1479.9605	3246.6984	0.0000	1.0000
GTRIG	45	-1479.1903	3251.6758	0.0000	1.0000
F81G	39	-1502.8975	3259.9842	0.0000	1.0000
F81I	39	-1502.9282	3260.0455	0.0000	1.0000
K2P	36	-1512.7616	3260.1594	0.0000	1.0000
SYMG	41	-1497.9202	3263.0649	0.0000	1.0000
SYMI	41	-1497.9515	3263.1275	0.0000	1.0000
F81IG	40	-1502.3046	3265.3160	0.0000	1.0000
GTR	43	-1493.4405	3267.1408	0.0000	1.0000
SYMIG	42	-1497.2830	3268.3081	0.0000	1.0000
JC69G	36	-1519.4709	3273.5779	0.0000	1.0000
JC69I	36	-1519.4910	3273.6181	0.0000	1.0000
JC69IG	37	-1518.9182	3278.9903	0.0000	1.0000
F81	38	-1516.5938	3280.8590	0.0000	1.0000
SYM	40	-1511.6016	3283.9101	0.0000	1.0000
JC69	35	-1533.2207	3294.5600	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/chr1_5281.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5281.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/chr1_5281.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5281.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_5281.phylip = 1 - 677;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5281.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

