
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:15 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_5441.phylip" (19 taxa, 702 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	-2114.1402	4322.3078	0.6604	0.6604
GTRIG	45	-2113.6739	4323.6589	0.3361	0.9964
GTRI	44	-2119.4290	4332.8853	0.0033	0.9998
HKYG	40	-2127.2145	4339.3911	0.0001	0.9999
HKYIG	41	-2126.3345	4339.8871	0.0001	1.0000
HKYI	40	-2131.0158	4346.9938	0.0000	1.0000
GTR	43	-2145.2542	4382.2592	0.0000	1.0000
SYMG	41	-2149.5820	4386.3821	0.0000	1.0000
SYMIG	42	-2148.6174	4386.7159	0.0000	1.0000
K2PG	37	-2156.1293	4390.4936	0.0000	1.0000
K2PIG	38	-2155.1826	4390.8357	0.0000	1.0000
SYMI	41	-2153.5804	4394.3790	0.0000	1.0000
HKY	39	-2157.2176	4397.1482	0.0000	1.0000
K2PI	37	-2160.0442	4398.3233	0.0000	1.0000
SYM	40	-2179.0558	4443.0737	0.0000	1.0000
K2P	36	-2186.1927	4448.3914	0.0000	1.0000
F81G	39	-2183.4968	4449.7066	0.0000	1.0000
F81IG	40	-2182.6366	4450.2355	0.0000	1.0000
F81I	39	-2187.6899	4458.0929	0.0000	1.0000
JC69G	36	-2205.4351	4486.8761	0.0000	1.0000
JC69IG	37	-2204.4466	4487.1280	0.0000	1.0000
JC69I	36	-2209.4955	4494.9970	0.0000	1.0000
F81	38	-2211.4260	4503.3225	0.0000	1.0000
JC69	35	-2234.5015	4542.7867	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2114.1402	4316.2804	0.6283	0.6283
GTRIG	45	-2113.6739	4317.3479	0.3684	0.9967
GTRI	44	-2119.4290	4326.8579	0.0032	0.9999
HKYG	40	-2127.2145	4334.4289	0.0001	0.9999
HKYIG	41	-2126.3345	4334.6690	0.0001	1.0000
HKYI	40	-2131.0158	4342.0316	0.0000	1.0000
GTR	43	-2145.2542	4376.5084	0.0000	1.0000
SYMG	41	-2149.5820	4381.1639	0.0000	1.0000
SYMIG	42	-2148.6174	4381.2349	0.0000	1.0000
K2PG	37	-2156.1293	4386.2587	0.0000	1.0000
K2PIG	38	-2155.1826	4386.3651	0.0000	1.0000
SYMI	41	-2153.5804	4389.1608	0.0000	1.0000
HKY	39	-2157.2176	4392.4352	0.0000	1.0000
K2PI	37	-2160.0442	4394.0884	0.0000	1.0000
SYM	40	-2179.0558	4438.1116	0.0000	1.0000
K2P	36	-2186.1927	4444.3853	0.0000	1.0000
F81G	39	-2183.4968	4444.9936	0.0000	1.0000
F81IG	40	-2182.6366	4445.2733	0.0000	1.0000
F81I	39	-2187.6899	4453.3799	0.0000	1.0000
JC69G	36	-2205.4351	4482.8701	0.0000	1.0000
JC69IG	37	-2204.4466	4482.8931	0.0000	1.0000
JC69I	36	-2209.4955	4490.9910	0.0000	1.0000
F81	38	-2211.4260	4498.8520	0.0000	1.0000
JC69	35	-2234.5015	4539.0029	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2127.2145	4516.5863	0.4666	0.4666
GTRG	44	-2114.1402	4516.6535	0.4511	0.9177
HKYIG	41	-2126.3345	4521.3802	0.0425	0.9602
GTRIG	45	-2113.6739	4522.2749	0.0271	0.9873
HKYI	40	-2131.0158	4524.1889	0.0104	0.9977
GTRI	44	-2119.4290	4527.2310	0.0023	1.0000
K2PG	37	-2156.1293	4554.7542	0.0000	1.0000
K2PIG	38	-2155.1826	4559.4146	0.0000	1.0000
K2PI	37	-2160.0442	4562.5839	0.0000	1.0000
SYMG	41	-2149.5820	4567.8752	0.0000	1.0000
HKY	39	-2157.2176	4570.0386	0.0000	1.0000
GTR	43	-2145.2542	4572.3276	0.0000	1.0000
SYMIG	42	-2148.6174	4572.5001	0.0000	1.0000
SYMI	41	-2153.5804	4575.8721	0.0000	1.0000
K2P	36	-2186.1927	4608.3269	0.0000	1.0000
SYM	40	-2179.0558	4620.2689	0.0000	1.0000
F81G	39	-2183.4968	4622.5970	0.0000	1.0000
F81IG	40	-2182.6366	4627.4306	0.0000	1.0000
F81I	39	-2187.6899	4630.9833	0.0000	1.0000
JC69G	36	-2205.4351	4646.8117	0.0000	1.0000
JC69IG	37	-2204.4466	4651.3886	0.0000	1.0000
JC69I	36	-2209.4955	4654.9326	0.0000	1.0000
F81	38	-2211.4260	4671.9014	0.0000	1.0000
JC69	35	-2234.5015	4698.3906	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/chr3_5441.phylip = 1 - 702;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5441.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/chr3_5441.phylip = 1 - 702;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5441.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/chr3_5441.phylip = 1 - 702;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5441.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

