
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:46 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_4403.phylip" (19 taxa, 483 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	-1872.5555	3842.1520	0.6194	0.6194
GTRIG	45	-1871.8289	3843.1314	0.3795	0.9989
HKYG	40	-1884.3607	3856.1422	0.0006	0.9995
HKYIG	41	-1883.6417	3857.0930	0.0004	0.9998
GTRI	44	-1880.8388	3858.7187	0.0002	1.0000
HKYI	40	-1888.7868	3864.9945	0.0000	1.0000
SYMG	41	-1900.6711	3891.1517	0.0000	1.0000
K2PG	37	-1905.8806	3892.0802	0.0000	1.0000
SYMIG	42	-1900.1351	3892.4793	0.0000	1.0000
K2PIG	38	-1905.2529	3893.1814	0.0000	1.0000
SYMI	41	-1902.5754	3894.9603	0.0000	1.0000
K2PI	37	-1907.5575	3895.4342	0.0000	1.0000
F81G	39	-1918.3041	3921.6510	0.0000	1.0000
F81IG	40	-1917.6565	3922.7338	0.0000	1.0000
F81I	39	-1920.8730	3926.7890	0.0000	1.0000
JC69G	36	-1935.7138	3949.4008	0.0000	1.0000
GTR	43	-1927.4863	3949.5922	0.0000	1.0000
JC69IG	37	-1935.0982	3950.5155	0.0000	1.0000
JC69I	36	-1936.8649	3951.7028	0.0000	1.0000
HKY	39	-1941.8333	3968.7094	0.0000	1.0000
SYM	40	-1958.2222	4003.8652	0.0000	1.0000
K2P	36	-1963.9805	4005.9341	0.0000	1.0000
F81	38	-1974.3962	4031.4680	0.0000	1.0000
JC69	35	-1993.9548	4063.5472	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1872.5555	3833.1109	0.5676	0.5676
GTRIG	45	-1871.8289	3833.6578	0.4318	0.9994
HKYG	40	-1884.3607	3848.7214	0.0002	0.9997
HKYIG	41	-1883.6417	3849.2835	0.0002	0.9999
GTRI	44	-1880.8388	3849.6776	0.0001	1.0000
HKYI	40	-1888.7868	3857.5737	0.0000	1.0000
SYMG	41	-1900.6711	3883.3422	0.0000	1.0000
SYMIG	42	-1900.1351	3884.2702	0.0000	1.0000
K2PG	37	-1905.8806	3885.7611	0.0000	1.0000
K2PIG	38	-1905.2529	3886.5057	0.0000	1.0000
SYMI	41	-1902.5754	3887.1508	0.0000	1.0000
K2PI	37	-1907.5575	3889.1151	0.0000	1.0000
F81G	39	-1918.3041	3914.6082	0.0000	1.0000
F81IG	40	-1917.6565	3915.3129	0.0000	1.0000
F81I	39	-1920.8730	3919.7461	0.0000	1.0000
GTR	43	-1927.4863	3940.9726	0.0000	1.0000
JC69G	36	-1935.7138	3943.4277	0.0000	1.0000
JC69IG	37	-1935.0982	3944.1964	0.0000	1.0000
JC69I	36	-1936.8649	3945.7297	0.0000	1.0000
HKY	39	-1941.8333	3961.6665	0.0000	1.0000
SYM	40	-1958.2222	3996.4443	0.0000	1.0000
K2P	36	-1963.9805	3999.9610	0.0000	1.0000
F81	38	-1974.3962	4024.7923	0.0000	1.0000
JC69	35	-1993.9548	4057.9096	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1884.3607	4015.9221	0.5768	0.5768
GTRG	44	-1872.5555	4017.0317	0.3312	0.9080
HKYIG	41	-1883.6417	4020.6642	0.0539	0.9618
GTRIG	45	-1871.8289	4021.7585	0.0312	0.9930
HKYI	40	-1888.7868	4024.7743	0.0069	0.9999
GTRI	44	-1880.8388	4033.5983	0.0001	1.0000
K2PG	37	-1905.8806	4040.4217	0.0000	1.0000
K2PI	37	-1907.5575	4043.7757	0.0000	1.0000
K2PIG	38	-1905.2529	4045.3464	0.0000	1.0000
SYMG	41	-1900.6711	4054.7228	0.0000	1.0000
SYMI	41	-1902.5754	4058.5314	0.0000	1.0000
SYMIG	42	-1900.1351	4059.8309	0.0000	1.0000
F81G	39	-1918.3041	4077.6288	0.0000	1.0000
F81IG	40	-1917.6565	4082.5136	0.0000	1.0000
F81I	39	-1920.8730	4082.7667	0.0000	1.0000
JC69G	36	-1935.7138	4093.9083	0.0000	1.0000
JC69I	36	-1936.8649	4096.2103	0.0000	1.0000
JC69IG	37	-1935.0982	4098.8570	0.0000	1.0000
GTR	43	-1927.4863	4120.7134	0.0000	1.0000
HKY	39	-1941.8333	4124.6872	0.0000	1.0000
K2P	36	-1963.9805	4150.4416	0.0000	1.0000
SYM	40	-1958.2222	4163.6450	0.0000	1.0000
F81	38	-1974.3962	4183.6329	0.0000	1.0000
JC69	35	-1993.9548	4204.2102	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/chr6_4403.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4403.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/chr6_4403.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4403.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/chr6_4403.phylip = 1 - 483;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4403.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

