
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:14 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/chr4_7559.phylip" (19 taxa, 705 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-1920.1445	3927.4837	0.3979	0.3979
HKYG	40	-1921.3688	3927.6773	0.3611	0.7590
HKYI	40	-1922.3221	3929.5840	0.1392	0.8982
K2PIG	38	-1926.1587	3932.7678	0.0283	0.9265
K2PG	37	-1927.5219	3933.2597	0.0222	0.9487
GTRIG	45	-1918.6901	3933.6625	0.0181	0.9668
GTRG	44	-1919.9199	3933.8398	0.0166	0.9834
K2PI	37	-1928.4491	3935.1141	0.0088	0.9922
GTRI	44	-1920.7941	3935.5881	0.0069	0.9991
SYMIG	42	-1925.8167	3941.0897	0.0004	0.9995
SYMG	41	-1927.1775	3941.5495	0.0004	0.9999
SYMI	41	-1928.1015	3943.3975	0.0001	1.0000
HKY	39	-1953.6893	3990.0704	0.0000	1.0000
K2P	36	-1960.0977	3996.1834	0.0000	1.0000
GTR	43	-1952.2840	3996.2928	0.0000	1.0000
SYM	40	-1958.9454	4002.8307	0.0000	1.0000
F81G	39	-1966.9111	4016.5138	0.0000	1.0000
F81IG	40	-1965.9325	4016.8047	0.0000	1.0000
F81I	39	-1968.0771	4018.8459	0.0000	1.0000
JC69IG	37	-1971.3733	4020.9625	0.0000	1.0000
JC69G	36	-1972.5919	4021.1719	0.0000	1.0000
JC69I	36	-1973.4972	4022.9824	0.0000	1.0000
F81	38	-1998.8105	4078.0714	0.0000	1.0000
JC69	35	-2004.3683	4082.5034	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1920.1445	3922.2891	0.4214	0.4214
HKYG	40	-1921.3688	3922.7376	0.3367	0.7581
HKYI	40	-1922.3221	3924.6442	0.1298	0.8879
GTRIG	45	-1918.6901	3927.3802	0.0330	0.9210
GTRG	44	-1919.9199	3927.8398	0.0263	0.9472
K2PIG	38	-1926.1587	3928.3174	0.0207	0.9679
K2PG	37	-1927.5219	3929.0438	0.0144	0.9823
GTRI	44	-1920.7941	3929.5881	0.0110	0.9933
K2PI	37	-1928.4491	3930.8982	0.0057	0.9989
SYMIG	42	-1925.8167	3935.6335	0.0005	0.9995
SYMG	41	-1927.1775	3936.3550	0.0004	0.9999
SYMI	41	-1928.1015	3938.2029	0.0001	1.0000
HKY	39	-1953.6893	3985.3786	0.0000	1.0000
GTR	43	-1952.2840	3990.5681	0.0000	1.0000
K2P	36	-1960.0977	3992.1954	0.0000	1.0000
SYM	40	-1958.9454	3997.8909	0.0000	1.0000
F81G	39	-1966.9111	4011.8221	0.0000	1.0000
F81IG	40	-1965.9325	4011.8649	0.0000	1.0000
F81I	39	-1968.0771	4014.1541	0.0000	1.0000
JC69IG	37	-1971.3733	4016.7466	0.0000	1.0000
JC69G	36	-1972.5919	4017.1839	0.0000	1.0000
JC69I	36	-1973.4972	4018.9944	0.0000	1.0000
F81	38	-1998.8105	4073.6209	0.0000	1.0000
JC69	35	-2004.3683	4078.7366	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1927.5219	4097.6971	0.6326	0.6326
K2PI	37	-1928.4491	4099.5516	0.2503	0.8828
K2PIG	38	-1926.1587	4101.5289	0.0931	0.9759
HKYG	40	-1921.3688	4105.0655	0.0159	0.9918
HKYI	40	-1922.3221	4106.9722	0.0061	0.9980
HKYIG	41	-1920.1445	4109.1752	0.0020	1.0000
SYMG	41	-1927.1775	4123.2411	0.0000	1.0000
SYMI	41	-1928.1015	4125.0890	0.0000	1.0000
SYMIG	42	-1925.8167	4127.0778	0.0000	1.0000
GTRG	44	-1919.9199	4128.4005	0.0000	1.0000
GTRI	44	-1920.7941	4130.1488	0.0000	1.0000
GTRIG	45	-1918.6901	4132.4991	0.0000	1.0000
K2P	36	-1960.0977	4156.2905	0.0000	1.0000
HKY	39	-1953.6893	4163.1484	0.0000	1.0000
SYM	40	-1958.9454	4180.2188	0.0000	1.0000
JC69G	36	-1972.5919	4181.2790	0.0000	1.0000
JC69I	36	-1973.4972	4183.0895	0.0000	1.0000
JC69IG	37	-1971.3733	4185.3999	0.0000	1.0000
GTR	43	-1952.2840	4186.5706	0.0000	1.0000
F81G	39	-1966.9111	4189.5918	0.0000	1.0000
F81I	39	-1968.0771	4191.9239	0.0000	1.0000
F81IG	40	-1965.9325	4194.1928	0.0000	1.0000
JC69	35	-2004.3683	4238.2735	0.0000	1.0000
F81	38	-1998.8105	4246.8324	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7559.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7559.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7559.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7559.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr4_7559.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7559.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;


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End of Output

