
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:27 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/chr6_3215.phylip" (19 taxa, 592 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	-2159.4753	4414.1900	0.5743	0.5743
GTRIG	45	-2159.2995	4416.1813	0.2122	0.7865
HKYG	40	-2165.6587	4417.2703	0.1231	0.9096
HKYIG	41	-2165.5792	4419.4202	0.0420	0.9516
GTRI	44	-2162.2423	4419.7240	0.0361	0.9877
HKYI	40	-2167.9629	4421.8786	0.0123	1.0000
K2PG	37	-2182.2958	4443.6675	0.0000	1.0000
SYMG	41	-2177.7810	4443.8239	0.0000	1.0000
K2PIG	38	-2182.2189	4445.7976	0.0000	1.0000
SYMIG	42	-2177.6127	4445.8046	0.0000	1.0000
K2PI	37	-2184.5291	4448.1340	0.0000	1.0000
SYMI	41	-2180.0306	4448.3230	0.0000	1.0000
F81G	39	-2186.8232	4457.2986	0.0000	1.0000
F81IG	40	-2186.7693	4459.4914	0.0000	1.0000
F81I	39	-2189.1439	4461.9400	0.0000	1.0000
JC69G	36	-2208.0346	4492.8692	0.0000	1.0000
JC69IG	37	-2207.9810	4495.0379	0.0000	1.0000
JC69I	36	-2210.1362	4497.0723	0.0000	1.0000
GTR	43	-2206.7534	4506.4120	0.0000	1.0000
HKY	39	-2214.0141	4511.6804	0.0000	1.0000
SYM	40	-2226.3784	4538.7097	0.0000	1.0000
K2P	36	-2231.6026	4540.0052	0.0000	1.0000
F81	38	-2233.7217	4548.8033	0.0000	1.0000
JC69	35	-2255.4331	4585.3985	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2159.4753	4406.9505	0.5987	0.5987
GTRIG	45	-2159.2995	4408.5989	0.2626	0.8613
HKYG	40	-2165.6587	4411.3175	0.0674	0.9288
GTRI	44	-2162.2423	4412.4845	0.0376	0.9664
HKYIG	41	-2165.5792	4413.1584	0.0269	0.9933
HKYI	40	-2167.9629	4415.9258	0.0067	1.0000
SYMG	41	-2177.7810	4437.5621	0.0000	1.0000
K2PG	37	-2182.2958	4438.5917	0.0000	1.0000
SYMIG	42	-2177.6127	4439.2253	0.0000	1.0000
K2PIG	38	-2182.2189	4440.4377	0.0000	1.0000
SYMI	41	-2180.0306	4442.0612	0.0000	1.0000
K2PI	37	-2184.5291	4443.0582	0.0000	1.0000
F81G	39	-2186.8232	4451.6464	0.0000	1.0000
F81IG	40	-2186.7693	4453.5386	0.0000	1.0000
F81I	39	-2189.1439	4456.2879	0.0000	1.0000
JC69G	36	-2208.0346	4488.0692	0.0000	1.0000
JC69IG	37	-2207.9810	4489.9621	0.0000	1.0000
JC69I	36	-2210.1362	4492.2723	0.0000	1.0000
GTR	43	-2206.7534	4499.5069	0.0000	1.0000
HKY	39	-2214.0141	4506.0282	0.0000	1.0000
SYM	40	-2226.3784	4532.7569	0.0000	1.0000
K2P	36	-2231.6026	4535.2052	0.0000	1.0000
F81	38	-2233.7217	4543.4434	0.0000	1.0000
JC69	35	-2255.4331	4580.8662	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2165.6587	4586.6577	0.8719	0.8719
HKYI	40	-2167.9629	4591.2660	0.0871	0.9590
HKYIG	41	-2165.5792	4592.8822	0.0388	0.9978
GTRG	44	-2159.4753	4599.8248	0.0012	0.9990
K2PG	37	-2182.2958	4600.7814	0.0007	0.9998
K2PI	37	-2184.5291	4605.2479	0.0001	0.9998
GTRI	44	-2162.2423	4605.3588	0.0001	0.9999
GTRIG	45	-2159.2995	4605.8567	0.0001	1.0000
K2PIG	38	-2182.2189	4607.0110	0.0000	1.0000
SYMG	41	-2177.7810	4617.2859	0.0000	1.0000
SYMI	41	-2180.0306	4621.7850	0.0000	1.0000
F81G	39	-2186.8232	4622.6031	0.0000	1.0000
SYMIG	42	-2177.6127	4623.3326	0.0000	1.0000
F81I	39	-2189.1439	4627.2446	0.0000	1.0000
F81IG	40	-2186.7693	4628.8788	0.0000	1.0000
JC69G	36	-2208.0346	4645.8755	0.0000	1.0000
JC69I	36	-2210.1362	4650.0786	0.0000	1.0000
JC69IG	37	-2207.9810	4652.1518	0.0000	1.0000
HKY	39	-2214.0141	4676.9850	0.0000	1.0000
GTR	43	-2206.7534	4687.9976	0.0000	1.0000
K2P	36	-2231.6026	4693.0115	0.0000	1.0000
SYM	40	-2226.3784	4708.0971	0.0000	1.0000
F81	38	-2233.7217	4710.0167	0.0000	1.0000
JC69	35	-2255.4331	4734.2889	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/chr6_3215.phylip = 1 - 592;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3215.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/chr6_3215.phylip = 1 - 592;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3215.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/chr6_3215.phylip = 1 - 592;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3215.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

