
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:06 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/chr13_2870.phylip" (19 taxa, 545 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1910.3680	3907.2439	0.6077	0.6077
HKYIG	41	-1910.2002	3909.2474	0.2232	0.8309
HKYI	40	-1912.0392	3910.5862	0.1143	0.9451
GTRG	44	-1908.5211	3912.9622	0.0348	0.9799
GTRIG	45	-1908.3079	3914.9124	0.0131	0.9931
GTRI	44	-1910.3160	3916.5521	0.0058	0.9989
K2PG	37	-1920.5010	3920.5484	0.0008	0.9997
K2PIG	38	-1920.3199	3922.4975	0.0003	1.0000
SYMG	41	-1919.1879	3927.2228	0.0000	1.0000
K2PI	37	-1924.4420	3928.4304	0.0000	1.0000
SYMI	41	-1921.1508	3931.1485	0.0000	1.0000
SYMIG	42	-1920.6162	3932.4276	0.0000	1.0000
HKY	39	-1938.2416	3960.6614	0.0000	1.0000
GTR	43	-1936.6863	3966.9254	0.0000	1.0000
K2P	36	-1949.1517	3975.5476	0.0000	1.0000
SYM	40	-1948.1626	3982.8332	0.0000	1.0000
F81G	39	-1972.7609	4029.7001	0.0000	1.0000
F81IG	40	-1972.6997	4031.9074	0.0000	1.0000
F81I	39	-1974.0813	4032.3409	0.0000	1.0000
JC69G	36	-1980.7587	4038.7615	0.0000	1.0000
JC69IG	37	-1983.4368	4046.4199	0.0000	1.0000
JC69I	36	-1985.4307	4048.1055	0.0000	1.0000
F81	38	-1998.6388	4079.1353	0.0000	1.0000
JC69	35	-2007.0999	4089.1506	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1910.3680	3900.7360	0.5517	0.5517
HKYIG	41	-1910.2002	3902.4005	0.2400	0.7917
HKYI	40	-1912.0392	3904.0783	0.1037	0.8954
GTRG	44	-1908.5211	3905.0422	0.0641	0.9595
GTRIG	45	-1908.3079	3906.6158	0.0292	0.9887
GTRI	44	-1910.3160	3908.6321	0.0106	0.9993
K2PG	37	-1920.5010	3915.0020	0.0004	0.9998
K2PIG	38	-1920.3199	3916.6398	0.0002	1.0000
SYMG	41	-1919.1879	3920.3759	0.0000	1.0000
K2PI	37	-1924.4420	3922.8840	0.0000	1.0000
SYMI	41	-1921.1508	3924.3016	0.0000	1.0000
SYMIG	42	-1920.6162	3925.2324	0.0000	1.0000
HKY	39	-1938.2416	3954.4831	0.0000	1.0000
GTR	43	-1936.6863	3959.3725	0.0000	1.0000
K2P	36	-1949.1517	3970.3035	0.0000	1.0000
SYM	40	-1948.1626	3976.3253	0.0000	1.0000
F81G	39	-1972.7609	4023.5218	0.0000	1.0000
F81IG	40	-1972.6997	4025.3995	0.0000	1.0000
F81I	39	-1974.0813	4026.1627	0.0000	1.0000
JC69G	36	-1980.7587	4033.5174	0.0000	1.0000
JC69IG	37	-1983.4368	4040.8735	0.0000	1.0000
JC69I	36	-1985.4307	4042.8614	0.0000	1.0000
F81	38	-1998.6388	4073.2776	0.0000	1.0000
JC69	35	-2007.0999	4084.1998	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1910.3680	4072.7674	0.5617	0.5617
K2PG	37	-1920.5010	4074.1311	0.2841	0.8458
HKYI	40	-1912.0392	4076.1097	0.1056	0.9514
HKYIG	41	-1910.2002	4078.7327	0.0285	0.9799
K2PIG	38	-1920.3199	4080.0696	0.0146	0.9945
K2PI	37	-1924.4420	4082.0131	0.0055	1.0000
GTRG	44	-1908.5211	4094.2768	0.0000	1.0000
SYMG	41	-1919.1879	4096.7081	0.0000	1.0000
GTRI	44	-1910.3160	4097.8667	0.0000	1.0000
GTRIG	45	-1908.3079	4100.1512	0.0000	1.0000
SYMI	41	-1921.1508	4100.6338	0.0000	1.0000
SYMIG	42	-1920.6162	4105.8654	0.0000	1.0000
HKY	39	-1938.2416	4122.2138	0.0000	1.0000
K2P	36	-1949.1517	4125.1318	0.0000	1.0000
GTR	43	-1936.6863	4144.3063	0.0000	1.0000
SYM	40	-1948.1626	4148.3567	0.0000	1.0000
JC69G	36	-1980.7587	4188.3457	0.0000	1.0000
F81G	39	-1972.7609	4191.2525	0.0000	1.0000
F81I	39	-1974.0813	4193.8933	0.0000	1.0000
F81IG	40	-1972.6997	4197.4309	0.0000	1.0000
JC69I	36	-1985.4307	4197.6897	0.0000	1.0000
JC69IG	37	-1983.4368	4200.0026	0.0000	1.0000
JC69	35	-2007.0999	4234.7273	0.0000	1.0000
F81	38	-1998.6388	4236.7074	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/chr13_2870.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2870.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2870.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2870.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2870.phylip = 1 - 545;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2870.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

