
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:04 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/chr3_17832.phylip" (19 taxa, 1155 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-4121.8014	8328.6972	0.5741	0.5741
HKYG	40	-4123.4096	8329.7635	0.3369	0.9110
GTRIG	45	-4119.7470	8333.2270	0.0596	0.9706
GTRG	44	-4121.5384	8334.6443	0.0294	1.0000
HKYI	40	-4134.5157	8351.9757	0.0000	1.0000
GTRI	44	-4133.7961	8359.1598	0.0000	1.0000
SYMIG	42	-4176.2627	8439.7737	0.0000	1.0000
K2PIG	38	-4183.6050	8445.8660	0.0000	1.0000
K2PG	37	-4184.9599	8446.4372	0.0000	1.0000
SYMG	41	-4184.3176	8453.7295	0.0000	1.0000
SYMI	41	-4185.3578	8455.8099	0.0000	1.0000
K2PI	37	-4190.8325	8458.1825	0.0000	1.0000
F81IG	40	-4215.3679	8513.6802	0.0000	1.0000
F81G	39	-4221.9161	8524.6304	0.0000	1.0000
F81I	39	-4225.0950	8530.9883	0.0000	1.0000
HKY	39	-4237.1622	8555.1227	0.0000	1.0000
GTR	43	-4234.6284	8558.6627	0.0000	1.0000
JC69IG	37	-4271.6548	8619.8272	0.0000	1.0000
JC69G	36	-4273.0734	8620.5296	0.0000	1.0000
JC69I	36	-4281.0731	8636.5290	0.0000	1.0000
SYM	40	-4301.0113	8684.9669	0.0000	1.0000
K2P	36	-4309.1376	8692.6579	0.0000	1.0000
F81	38	-4337.0019	8752.6598	0.0000	1.0000
JC69	35	-4386.9932	8846.2384	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-4121.8014	8325.6029	0.5708	0.5708
HKYG	40	-4123.4096	8326.8191	0.3107	0.8815
GTRIG	45	-4119.7470	8329.4939	0.0816	0.9630
GTRG	44	-4121.5384	8331.0767	0.0370	1.0000
HKYI	40	-4134.5157	8349.0314	0.0000	1.0000
GTRI	44	-4133.7961	8355.5922	0.0000	1.0000
SYMIG	42	-4176.2627	8436.5255	0.0000	1.0000
K2PIG	38	-4183.6050	8443.2100	0.0000	1.0000
K2PG	37	-4184.9599	8443.9197	0.0000	1.0000
SYMG	41	-4184.3176	8450.6351	0.0000	1.0000
SYMI	41	-4185.3578	8452.7156	0.0000	1.0000
K2PI	37	-4190.8325	8455.6650	0.0000	1.0000
F81IG	40	-4215.3679	8510.7358	0.0000	1.0000
F81G	39	-4221.9161	8521.8322	0.0000	1.0000
F81I	39	-4225.0950	8528.1901	0.0000	1.0000
HKY	39	-4237.1622	8552.3245	0.0000	1.0000
GTR	43	-4234.6284	8555.2568	0.0000	1.0000
JC69IG	37	-4271.6548	8617.3097	0.0000	1.0000
JC69G	36	-4273.0734	8618.1467	0.0000	1.0000
JC69I	36	-4281.0731	8634.1462	0.0000	1.0000
SYM	40	-4301.0113	8682.0226	0.0000	1.0000
K2P	36	-4309.1376	8690.2751	0.0000	1.0000
F81	38	-4337.0019	8750.0039	0.0000	1.0000
JC69	35	-4386.9932	8843.9864	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4123.4096	8528.8933	0.8719	0.8719
HKYIG	41	-4121.8014	8532.7290	0.1281	1.0000
HKYI	40	-4134.5157	8551.1056	0.0000	1.0000
GTRG	44	-4121.5384	8553.3584	0.0000	1.0000
GTRIG	45	-4119.7470	8556.8274	0.0000	1.0000
GTRI	44	-4133.7961	8577.8739	0.0000	1.0000
K2PG	37	-4184.9599	8630.8384	0.0000	1.0000
K2PIG	38	-4183.6050	8635.1806	0.0000	1.0000
K2PI	37	-4190.8325	8642.5837	0.0000	1.0000
SYMIG	42	-4176.2627	8648.7034	0.0000	1.0000
SYMG	41	-4184.3176	8657.7612	0.0000	1.0000
SYMI	41	-4185.3578	8659.8417	0.0000	1.0000
F81IG	40	-4215.3679	8712.8100	0.0000	1.0000
F81G	39	-4221.9161	8718.8545	0.0000	1.0000
F81I	39	-4225.0950	8725.2124	0.0000	1.0000
HKY	39	-4237.1622	8749.3468	0.0000	1.0000
GTR	43	-4234.6284	8772.4866	0.0000	1.0000
JC69G	36	-4273.0734	8800.0135	0.0000	1.0000
JC69IG	37	-4271.6548	8804.2284	0.0000	1.0000
JC69I	36	-4281.0731	8816.0130	0.0000	1.0000
K2P	36	-4309.1376	8872.1419	0.0000	1.0000
SYM	40	-4301.0113	8884.0968	0.0000	1.0000
F81	38	-4337.0019	8941.9744	0.0000	1.0000
JC69	35	-4386.9932	9020.8013	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17832.phylip = 1 - 1155;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17832.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17832.phylip = 1 - 1155;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17832.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr3_17832.phylip = 1 - 1155;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17832.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

