
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:43 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_4101.phylip" (19 taxa, 382 characters)

Minimum AIC  model: HKYG
Minimum AICc model: K2PG
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
K2PG	37	-979.3154	2040.8052	0.2090	0.2090
HKYG	40	-975.6113	2040.8413	0.2053	0.4143
K2PI	37	-979.6343	2041.4429	0.1519	0.5662
HKYI	40	-975.9299	2041.4786	0.1492	0.7154
K2PIG	38	-978.7894	2042.2203	0.1030	0.8185
HKYIG	41	-975.1605	2042.4505	0.0918	0.9103
GTRG	44	-972.4691	2044.6890	0.0300	0.9402
GTRI	44	-972.8486	2045.4480	0.0205	0.9607
SYMG	41	-977.1372	2046.4039	0.0127	0.9735
GTRIG	45	-972.1052	2046.5317	0.0119	0.9854
SYMI	41	-977.4833	2047.0961	0.0090	0.9944
SYMIG	42	-976.6938	2048.0426	0.0056	1.0000
HKY	39	-990.0218	2067.1664	0.0000	1.0000
GTR	43	-985.4263	2068.0479	0.0000	1.0000
K2P	36	-994.4524	2068.6266	0.0000	1.0000
SYM	40	-990.7439	2071.1066	0.0000	1.0000
JC69G	36	-1000.9056	2081.5329	0.0000	1.0000
F81G	39	-997.3119	2081.7466	0.0000	1.0000
JC69I	36	-1001.1124	2081.9465	0.0000	1.0000
F81I	39	-997.5142	2082.1512	0.0000	1.0000
JC69IG	37	-1000.6359	2083.4462	0.0000	1.0000
F81IG	40	-997.0829	2083.7846	0.0000	1.0000
F81	38	-1010.7062	2106.0537	0.0000	1.0000
JC69	35	-1014.7013	2106.6859	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-975.6113	2031.2225	0.2180	0.2180
HKYI	40	-975.9299	2031.8599	0.1585	0.3765
HKYIG	41	-975.1605	2032.3210	0.1259	0.5023
K2PG	37	-979.3154	2032.6308	0.1078	0.6101
GTRG	44	-972.4691	2032.9383	0.0924	0.7026
K2PI	37	-979.6343	2033.2685	0.0784	0.7810
K2PIG	38	-978.7894	2033.5789	0.0671	0.8481
GTRI	44	-972.8486	2033.6972	0.0632	0.9113
GTRIG	45	-972.1052	2034.2103	0.0489	0.9602
SYMG	41	-977.1372	2036.2744	0.0174	0.9777
SYMI	41	-977.4833	2036.9667	0.0123	0.9900
SYMIG	42	-976.6938	2037.3877	0.0100	1.0000
GTR	43	-985.4263	2056.8526	0.0000	1.0000
HKY	39	-990.0218	2058.0436	0.0000	1.0000
K2P	36	-994.4524	2060.9049	0.0000	1.0000
SYM	40	-990.7439	2061.4878	0.0000	1.0000
F81G	39	-997.3119	2072.6238	0.0000	1.0000
F81I	39	-997.5142	2073.0284	0.0000	1.0000
JC69G	36	-1000.9056	2073.8112	0.0000	1.0000
F81IG	40	-997.0829	2074.1658	0.0000	1.0000
JC69I	36	-1001.1124	2074.2247	0.0000	1.0000
JC69IG	37	-1000.6359	2075.2718	0.0000	1.0000
F81	38	-1010.7062	2097.4123	0.0000	1.0000
JC69	35	-1014.7013	2099.4026	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-979.3154	2178.6114	0.5484	0.5484
K2PI	37	-979.6343	2179.2491	0.3987	0.9471
K2PIG	38	-978.7894	2183.5049	0.0475	0.9945
HKYG	40	-975.6113	2189.0393	0.0030	0.9975
HKYI	40	-975.9299	2189.6767	0.0022	0.9997
HKYIG	41	-975.1605	2194.0833	0.0002	0.9999
SYMG	41	-977.1372	2198.0367	0.0000	1.0000
SYMI	41	-977.4833	2198.7289	0.0000	1.0000
K2P	36	-994.4524	2202.9400	0.0000	1.0000
SYMIG	42	-976.6938	2203.0954	0.0000	1.0000
GTRG	44	-972.4691	2206.5368	0.0000	1.0000
GTRI	44	-972.8486	2207.2957	0.0000	1.0000
GTRIG	45	-972.1052	2211.7542	0.0000	1.0000
HKY	39	-990.0218	2211.9150	0.0000	1.0000
JC69G	36	-1000.9056	2215.8463	0.0000	1.0000
JC69I	36	-1001.1124	2216.2599	0.0000	1.0000
SYM	40	-990.7439	2219.3046	0.0000	1.0000
JC69IG	37	-1000.6359	2221.2523	0.0000	1.0000
F81G	39	-997.3119	2226.4952	0.0000	1.0000
GTR	43	-985.4263	2226.5057	0.0000	1.0000
F81I	39	-997.5142	2226.8998	0.0000	1.0000
F81IG	40	-997.0829	2231.9826	0.0000	1.0000
JC69	35	-1014.7013	2237.4923	0.0000	1.0000
F81	38	-1010.7062	2247.3383	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4101.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4101.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;


[Mrbayes block for the best AICc model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4101.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4101.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;


[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/chr6_4101.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4101.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;


-------------------------------------------------------------
End of Output

