
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:09 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/chr7_11485.phylip" (19 taxa, 833 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-4212.9046	8518.8345	0.7018	0.7018
GTRIG	45	-4212.7333	8520.7271	0.2724	0.9742
HKYG	40	-4221.0709	8526.2831	0.0169	0.9911
HKYIG	41	-4220.6090	8527.5721	0.0089	1.0000
GTRI	44	-4228.1601	8549.3457	0.0000	1.0000
HKYI	40	-4233.5700	8551.2814	0.0000	1.0000
K2PG	37	-4259.8700	8597.2771	0.0000	1.0000
K2PIG	38	-4258.9101	8597.5533	0.0000	1.0000
SYMG	41	-4256.7827	8599.9194	0.0000	1.0000
SYMIG	42	-4255.9841	8600.5403	0.0000	1.0000
K2PI	37	-4270.1500	8617.8370	0.0000	1.0000
SYMI	41	-4268.0514	8622.4568	0.0000	1.0000
GTR	43	-4318.9410	8728.6779	0.0000	1.0000
HKY	39	-4326.7465	8735.4275	0.0000	1.0000
F81G	39	-4335.6177	8753.1698	0.0000	1.0000
F81IG	40	-4335.0349	8754.2112	0.0000	1.0000
F81I	39	-4346.4628	8774.8600	0.0000	1.0000
JC69G	36	-4361.9944	8799.3356	0.0000	1.0000
JC69IG	37	-4361.2290	8799.9951	0.0000	1.0000
K2P	36	-4368.8206	8812.9879	0.0000	1.0000
SYM	40	-4366.1311	8816.4037	0.0000	1.0000
JC69I	36	-4372.4646	8820.2759	0.0000	1.0000
F81	38	-4435.1417	8950.0165	0.0000	1.0000
JC69	35	-4464.2548	9001.6714	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4212.9046	8513.8092	0.6844	0.6844
GTRIG	45	-4212.7333	8515.4666	0.2988	0.9832
HKYG	40	-4221.0709	8522.1417	0.0106	0.9938
HKYIG	41	-4220.6090	8523.2181	0.0062	1.0000
GTRI	44	-4228.1601	8544.3203	0.0000	1.0000
HKYI	40	-4233.5700	8547.1399	0.0000	1.0000
K2PG	37	-4259.8700	8593.7400	0.0000	1.0000
K2PIG	38	-4258.9101	8593.8203	0.0000	1.0000
SYMG	41	-4256.7827	8595.5654	0.0000	1.0000
SYMIG	42	-4255.9841	8595.9682	0.0000	1.0000
K2PI	37	-4270.1500	8614.2999	0.0000	1.0000
SYMI	41	-4268.0514	8618.1028	0.0000	1.0000
GTR	43	-4318.9410	8723.8820	0.0000	1.0000
HKY	39	-4326.7465	8731.4930	0.0000	1.0000
F81G	39	-4335.6177	8749.2354	0.0000	1.0000
F81IG	40	-4335.0349	8750.0698	0.0000	1.0000
F81I	39	-4346.4628	8770.9256	0.0000	1.0000
JC69G	36	-4361.9944	8795.9888	0.0000	1.0000
JC69IG	37	-4361.2290	8796.4580	0.0000	1.0000
K2P	36	-4368.8206	8809.6412	0.0000	1.0000
SYM	40	-4366.1311	8812.2623	0.0000	1.0000
JC69I	36	-4372.4646	8816.9292	0.0000	1.0000
F81	38	-4435.1417	8946.2835	0.0000	1.0000
JC69	35	-4464.2548	8998.5096	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4221.0709	8711.1431	0.9432	0.9432
HKYIG	41	-4220.6090	8716.9445	0.0519	0.9950
GTRG	44	-4212.9046	8721.7106	0.0048	0.9998
GTRIG	45	-4212.7333	8728.0931	0.0002	1.0000
HKYI	40	-4233.5700	8736.1413	0.0000	1.0000
GTRI	44	-4228.1601	8752.2218	0.0000	1.0000
K2PG	37	-4259.8700	8768.5662	0.0000	1.0000
K2PIG	38	-4258.9101	8773.3715	0.0000	1.0000
K2PI	37	-4270.1500	8789.1262	0.0000	1.0000
SYMG	41	-4256.7827	8789.2918	0.0000	1.0000
SYMIG	42	-4255.9841	8794.4196	0.0000	1.0000
SYMI	41	-4268.0514	8811.8292	0.0000	1.0000
HKY	39	-4326.7465	8915.7694	0.0000	1.0000
GTR	43	-4318.9410	8927.0584	0.0000	1.0000
F81G	39	-4335.6177	8933.5117	0.0000	1.0000
F81IG	40	-4335.0349	8939.0711	0.0000	1.0000
F81I	39	-4346.4628	8955.2019	0.0000	1.0000
JC69G	36	-4361.9944	8966.0901	0.0000	1.0000
JC69IG	37	-4361.2290	8971.2842	0.0000	1.0000
K2P	36	-4368.8206	8979.7424	0.0000	1.0000
JC69I	36	-4372.4646	8987.0304	0.0000	1.0000
SYM	40	-4366.1311	9001.2636	0.0000	1.0000
F81	38	-4435.1417	9125.8348	0.0000	1.0000
JC69	35	-4464.2548	9163.8857	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/chr7_11485.phylip = 1 - 833;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11485.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/chr7_11485.phylip = 1 - 833;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11485.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11485.phylip = 1 - 833;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11485.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

