
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:01 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/chr2_7963.phylip" (19 taxa, 345 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKY


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	-911.9350	1925.0700	0.2376	0.2376
GTRI	44	-911.9768	1925.1536	0.2279	0.4655
GTR	43	-913.5320	1925.6353	0.1791	0.6446
HKY	39	-919.3777	1926.9849	0.0912	0.7359
HKYG	40	-918.1170	1927.0234	0.0895	0.8253
HKYI	40	-918.1448	1927.0792	0.0870	0.9123
GTRIG	45	-911.9389	1927.7240	0.0630	0.9754
HKYIG	41	-918.1191	1929.6045	0.0246	1.0000
F81	38	-932.6347	1950.9557	0.0000	1.0000
F81G	39	-931.5199	1951.2693	0.0000	1.0000
F81I	39	-931.5308	1951.2910	0.0000	1.0000
F81IG	40	-931.5197	1953.8290	0.0000	1.0000
K2P	36	-939.9313	1960.5119	0.0000	1.0000
K2PG	37	-938.6872	1960.5340	0.0000	1.0000
K2PI	37	-938.7347	1960.6290	0.0000	1.0000
K2PIG	38	-938.6912	1963.0688	0.0000	1.0000
SYM	40	-936.5458	1963.8810	0.0000	1.0000
SYMG	41	-935.4373	1964.2409	0.0000	1.0000
SYMI	41	-935.4994	1964.3652	0.0000	1.0000
SYMIG	42	-935.4448	1966.8499	0.0000	1.0000
JC69	35	-950.6052	1979.3658	0.0000	1.0000
JC69G	36	-949.4789	1979.6072	0.0000	1.0000
JC69I	36	-949.5035	1979.6563	0.0000	1.0000
JC69IG	37	-949.4805	1982.1205	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-911.9350	1911.8700	0.3099	0.3099
GTRI	44	-911.9768	1911.9536	0.2972	0.6071
GTR	43	-913.5320	1913.0639	0.1706	0.7777
GTRIG	45	-911.9389	1913.8778	0.1136	0.8913
HKYG	40	-918.1170	1916.2339	0.0350	0.9262
HKYI	40	-918.1448	1916.2897	0.0340	0.9602
HKY	39	-919.3777	1916.7554	0.0269	0.9872
HKYIG	41	-918.1191	1918.2381	0.0128	1.0000
F81G	39	-931.5199	1941.0398	0.0000	1.0000
F81I	39	-931.5308	1941.0615	0.0000	1.0000
F81	38	-932.6347	1941.2694	0.0000	1.0000
F81IG	40	-931.5197	1943.0395	0.0000	1.0000
K2PG	37	-938.6872	1951.3744	0.0000	1.0000
K2PI	37	-938.7347	1951.4694	0.0000	1.0000
K2P	36	-939.9313	1951.8626	0.0000	1.0000
SYMG	41	-935.4373	1952.8745	0.0000	1.0000
SYMI	41	-935.4994	1952.9989	0.0000	1.0000
SYM	40	-936.5458	1953.0915	0.0000	1.0000
K2PIG	38	-938.6912	1953.3825	0.0000	1.0000
SYMIG	42	-935.4448	1954.8897	0.0000	1.0000
JC69G	36	-949.4789	1970.9579	0.0000	1.0000
JC69I	36	-949.5035	1971.0070	0.0000	1.0000
JC69	35	-950.6052	1971.2105	0.0000	1.0000
JC69IG	37	-949.4805	1972.9609	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-919.3777	2066.6537	0.7197	0.7197
HKYG	40	-918.1170	2069.9757	0.1367	0.8565
HKYI	40	-918.1448	2070.0315	0.1330	0.9894
HKYIG	41	-918.1191	2075.8234	0.0073	0.9968
GTR	43	-913.5320	2078.3363	0.0021	0.9988
GTRG	44	-911.9350	2080.9859	0.0006	0.9994
GTRI	44	-911.9768	2081.0695	0.0005	0.9999
GTRIG	45	-911.9389	2086.8373	0.0000	1.0000
F81	38	-932.6347	2087.3241	0.0000	1.0000
K2P	36	-939.9313	2090.2302	0.0000	1.0000
F81G	39	-931.5199	2090.9380	0.0000	1.0000
F81I	39	-931.5308	2090.9597	0.0000	1.0000
K2PG	37	-938.6872	2093.5855	0.0000	1.0000
K2PI	37	-938.7347	2093.6806	0.0000	1.0000
F81IG	40	-931.5197	2096.7813	0.0000	1.0000
K2PIG	38	-938.6912	2099.4372	0.0000	1.0000
JC69	35	-950.6052	2105.7345	0.0000	1.0000
SYM	40	-936.5458	2106.8333	0.0000	1.0000
JC69G	36	-949.4789	2109.3255	0.0000	1.0000
JC69I	36	-949.5035	2109.3746	0.0000	1.0000
SYMG	41	-935.4373	2110.4599	0.0000	1.0000
SYMI	41	-935.4994	2110.5842	0.0000	1.0000
JC69IG	37	-949.4805	2115.1720	0.0000	1.0000
SYMIG	42	-935.4448	2116.3185	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/chr2_7963.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7963.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/chr2_7963.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7963.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 (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7963.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7963.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

