
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:42 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_10520.phylip" (19 taxa, 345 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	-903.2446	1907.6892	0.2734	0.2734
HKYG	40	-908.5539	1907.8973	0.2464	0.5197
HKYI	40	-908.9371	1908.6636	0.1679	0.6877
GTRI	44	-903.7644	1908.7287	0.1626	0.8502
GTRIG	45	-903.1715	1910.1892	0.0783	0.9285
HKYIG	41	-908.5053	1910.3768	0.0713	0.9999
HKY	39	-917.8913	1924.0120	0.0001	0.9999
GTR	43	-913.1067	1924.7848	0.0001	1.0000
K2PG	37	-923.0582	1929.2760	0.0000	1.0000
K2PI	37	-923.3971	1929.9538	0.0000	1.0000
K2PIG	38	-922.9995	1931.6854	0.0000	1.0000
SYMG	41	-920.5771	1934.5206	0.0000	1.0000
SYMI	41	-920.9461	1935.2585	0.0000	1.0000
SYMIG	42	-920.5230	1937.0063	0.0000	1.0000
K2P	36	-932.6294	1945.9082	0.0000	1.0000
SYM	40	-930.0373	1950.8640	0.0000	1.0000
F81G	39	-933.1096	1954.4486	0.0000	1.0000
F81I	39	-933.3842	1954.9980	0.0000	1.0000
F81IG	40	-933.0791	1956.9477	0.0000	1.0000
F81	38	-942.0614	1969.8091	0.0000	1.0000
JC69G	36	-945.0961	1970.8416	0.0000	1.0000
JC69I	36	-945.3677	1971.3848	0.0000	1.0000
JC69IG	37	-945.0613	1973.2821	0.0000	1.0000
JC69	35	-954.2154	1986.5861	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-903.2446	1894.4892	0.3923	0.3923
GTRI	44	-903.7644	1895.5287	0.2333	0.6256
GTRIG	45	-903.1715	1896.3430	0.1553	0.7809
HKYG	40	-908.5539	1897.1078	0.1059	0.8868
HKYI	40	-908.9371	1897.8741	0.0722	0.9590
HKYIG	41	-908.5053	1899.0105	0.0409	0.9999
GTR	43	-913.1067	1912.2133	0.0001	1.0000
HKY	39	-917.8913	1913.7825	0.0000	1.0000
K2PG	37	-923.0582	1920.1164	0.0000	1.0000
K2PI	37	-923.3971	1920.7942	0.0000	1.0000
K2PIG	38	-922.9995	1921.9991	0.0000	1.0000
SYMG	41	-920.5771	1923.1542	0.0000	1.0000
SYMI	41	-920.9461	1923.8922	0.0000	1.0000
SYMIG	42	-920.5230	1925.0460	0.0000	1.0000
K2P	36	-932.6294	1937.2589	0.0000	1.0000
SYM	40	-930.0373	1940.0745	0.0000	1.0000
F81G	39	-933.1096	1944.2191	0.0000	1.0000
F81I	39	-933.3842	1944.7685	0.0000	1.0000
F81IG	40	-933.0791	1946.1582	0.0000	1.0000
F81	38	-942.0614	1960.1228	0.0000	1.0000
JC69G	36	-945.0961	1962.1923	0.0000	1.0000
JC69I	36	-945.3677	1962.7355	0.0000	1.0000
JC69IG	37	-945.0613	1964.1225	0.0000	1.0000
JC69	35	-954.2154	1978.4308	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-908.5539	2050.8496	0.5720	0.5720
HKYI	40	-908.9371	2051.6159	0.3899	0.9619
HKYIG	41	-908.5053	2056.5958	0.0323	0.9942
K2PG	37	-923.0582	2062.3275	0.0018	0.9960
K2PI	37	-923.3971	2063.0053	0.0013	0.9973
GTRG	44	-903.2446	2063.6052	0.0010	0.9983
HKY	39	-917.8913	2063.6808	0.0009	0.9993
GTRI	44	-903.7644	2064.6447	0.0006	0.9998
K2PIG	38	-922.9995	2068.0538	0.0001	0.9999
GTRIG	45	-903.1715	2069.3025	0.0001	1.0000
K2P	36	-932.6294	2075.6265	0.0000	1.0000
GTR	43	-913.1067	2077.4857	0.0000	1.0000
SYMG	41	-920.5771	2080.7395	0.0000	1.0000
SYMI	41	-920.9461	2081.4775	0.0000	1.0000
SYMIG	42	-920.5230	2086.4749	0.0000	1.0000
SYM	40	-930.0373	2093.8163	0.0000	1.0000
F81G	39	-933.1096	2094.1174	0.0000	1.0000
F81I	39	-933.3842	2094.6667	0.0000	1.0000
F81IG	40	-933.0791	2099.9000	0.0000	1.0000
JC69G	36	-945.0961	2100.5599	0.0000	1.0000
JC69I	36	-945.3677	2101.1031	0.0000	1.0000
F81	38	-942.0614	2106.1775	0.0000	1.0000
JC69IG	37	-945.0613	2106.3337	0.0000	1.0000
JC69	35	-954.2154	2112.9548	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_10520.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10520.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_10520.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10520.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_10520.phylip = 1 - 345;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10520.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

