
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:06 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/chr2_5499.phylip" (19 taxa, 499 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1554.5145	3205.7514	0.3203	0.3203
GTRI	44	-1554.8156	3206.3537	0.2370	0.5572
GTRIG	45	-1554.5214	3208.1819	0.0950	0.6522
K2PG	37	-1564.2234	3208.5465	0.0792	0.7314
HKYG	40	-1560.6986	3208.5588	0.0787	0.8101
HKYI	40	-1561.1020	3209.3655	0.0526	0.8627
K2PI	37	-1564.9290	3209.9578	0.0391	0.9018
SYMG	41	-1560.6090	3210.7541	0.0263	0.9280
K2PIG	38	-1564.2029	3210.8493	0.0250	0.9530
HKYIG	41	-1560.6896	3210.9152	0.0242	0.9773
SYMI	41	-1561.1888	3211.9136	0.0147	0.9920
SYMIG	42	-1560.6003	3213.1216	0.0080	1.0000
K2P	36	-1579.0380	3235.8422	0.0000	1.0000
HKY	39	-1575.6653	3236.1279	0.0000	1.0000
GTR	43	-1571.3117	3236.9399	0.0000	1.0000
SYM	40	-1576.2234	3239.6084	0.0000	1.0000
JC69G	36	-1588.5854	3254.9371	0.0000	1.0000
JC69I	36	-1589.1759	3256.1181	0.0000	1.0000
F81G	39	-1585.9099	3256.6173	0.0000	1.0000
JC69IG	37	-1588.5744	3257.2486	0.0000	1.0000
F81I	39	-1586.2754	3257.3482	0.0000	1.0000
F81IG	40	-1585.9039	3258.9694	0.0000	1.0000
JC69	35	-1602.3454	3280.1335	0.0000	1.0000
F81	38	-1599.6124	3281.6683	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1554.5145	3197.0289	0.3926	0.3926
GTRI	44	-1554.8156	3197.6312	0.2905	0.6832
GTRIG	45	-1554.5214	3199.0429	0.1434	0.8266
HKYG	40	-1560.6986	3201.3972	0.0442	0.8708
HKYI	40	-1561.1020	3202.2039	0.0295	0.9004
K2PG	37	-1564.2234	3202.4468	0.0262	0.9265
SYMG	41	-1560.6090	3203.2180	0.0178	0.9443
HKYIG	41	-1560.6896	3203.3791	0.0164	0.9607
K2PI	37	-1564.9290	3203.8580	0.0129	0.9736
SYMI	41	-1561.1888	3204.3775	0.0100	0.9836
K2PIG	38	-1564.2029	3204.4058	0.0098	0.9934
SYMIG	42	-1560.6003	3205.2006	0.0066	1.0000
GTR	43	-1571.3117	3228.6234	0.0000	1.0000
HKY	39	-1575.6653	3229.3305	0.0000	1.0000
K2P	36	-1579.0380	3230.0759	0.0000	1.0000
SYM	40	-1576.2234	3232.4468	0.0000	1.0000
JC69G	36	-1588.5854	3249.1709	0.0000	1.0000
F81G	39	-1585.9099	3249.8199	0.0000	1.0000
JC69I	36	-1589.1759	3250.3518	0.0000	1.0000
F81I	39	-1586.2754	3250.5508	0.0000	1.0000
JC69IG	37	-1588.5744	3251.1489	0.0000	1.0000
F81IG	40	-1585.9039	3251.8078	0.0000	1.0000
JC69	35	-1602.3454	3274.6907	0.0000	1.0000
F81	38	-1599.6124	3275.2248	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1564.2234	3358.3132	0.6473	0.6473
K2PI	37	-1564.9290	3359.7244	0.3196	0.9669
K2PIG	38	-1564.2029	3364.4848	0.0296	0.9965
HKYG	40	-1560.6986	3369.9014	0.0020	0.9984
HKYI	40	-1561.1020	3370.7082	0.0013	0.9997
SYMG	41	-1560.6090	3375.9349	0.0001	0.9998
HKYIG	41	-1560.6896	3376.0959	0.0001	0.9999
SYMI	41	-1561.1888	3377.0943	0.0001	1.0000
K2P	36	-1579.0380	3381.7297	0.0000	1.0000
SYMIG	42	-1560.6003	3382.1300	0.0000	1.0000
GTRG	44	-1554.5145	3382.3836	0.0000	1.0000
GTRI	44	-1554.8156	3382.9859	0.0000	1.0000
GTRIG	45	-1554.5214	3388.6101	0.0000	1.0000
HKY	39	-1575.6653	3393.6221	0.0000	1.0000
JC69G	36	-1588.5854	3400.8247	0.0000	1.0000
SYM	40	-1576.2234	3400.9510	0.0000	1.0000
JC69I	36	-1589.1759	3402.0056	0.0000	1.0000
JC69IG	37	-1588.5744	3407.0153	0.0000	1.0000
GTR	43	-1571.3117	3409.7655	0.0000	1.0000
F81G	39	-1585.9099	3414.1115	0.0000	1.0000
F81I	39	-1586.2754	3414.8424	0.0000	1.0000
F81IG	40	-1585.9039	3420.3121	0.0000	1.0000
JC69	35	-1602.3454	3422.1319	0.0000	1.0000
F81	38	-1599.6124	3435.3038	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/chr2_5499.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5499.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5499.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5499.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 BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5499.phylip = 1 - 499;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_5499.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

