
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:20 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/chr11_6481.phylip" (19 taxa, 601 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	-1929.1892	3953.5007	0.6310	0.6310
GTRIG	45	-1929.1945	3955.8484	0.1951	0.8261
GTRI	44	-1931.0247	3957.1717	0.1007	0.9268
HKYG	40	-1936.3394	3958.5359	0.0509	0.9776
HKYIG	41	-1936.3380	3960.8369	0.0161	0.9938
HKYI	40	-1938.4375	3962.7321	0.0062	1.0000
GTR	43	-1944.9713	3982.7362	0.0000	1.0000
SYMG	41	-1950.7416	3989.6442	0.0000	1.0000
HKY	39	-1953.4795	3990.5205	0.0000	1.0000
SYMIG	42	-1950.7413	3991.9558	0.0000	1.0000
SYMI	41	-1952.4035	3992.9680	0.0000	1.0000
K2PG	37	-1957.9396	3994.8739	0.0000	1.0000
K2PIG	38	-1957.9374	3997.1489	0.0000	1.0000
K2PI	37	-1959.7757	3998.5461	0.0000	1.0000
SYM	40	-1966.5223	4018.9017	0.0000	1.0000
K2P	36	-1974.7250	4026.1735	0.0000	1.0000
F81G	39	-1999.9672	4083.4960	0.0000	1.0000
F81IG	40	-1999.9670	4085.7912	0.0000	1.0000
F81I	39	-2001.2877	4086.1369	0.0000	1.0000
JC69G	36	-2016.4631	4109.6495	0.0000	1.0000
F81	38	-2015.5610	4112.3961	0.0000	1.0000
JC69IG	37	-2018.0368	4115.0682	0.0000	1.0000
JC69I	36	-2019.2268	4115.1770	0.0000	1.0000
JC69	35	-2031.5896	4137.6394	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1929.1892	3946.3784	0.6292	0.6292
GTRIG	45	-1929.1945	3948.3890	0.2302	0.8594
GTRI	44	-1931.0247	3950.0494	0.1004	0.9598
HKYG	40	-1936.3394	3952.6787	0.0270	0.9868
HKYIG	41	-1936.3380	3954.6759	0.0099	0.9967
HKYI	40	-1938.4375	3956.8750	0.0033	1.0000
GTR	43	-1944.9713	3975.9427	0.0000	1.0000
SYMG	41	-1950.7416	3983.4832	0.0000	1.0000
HKY	39	-1953.4795	3984.9590	0.0000	1.0000
SYMIG	42	-1950.7413	3985.4826	0.0000	1.0000
SYMI	41	-1952.4035	3986.8070	0.0000	1.0000
K2PG	37	-1957.9396	3989.8793	0.0000	1.0000
K2PIG	38	-1957.9374	3991.8749	0.0000	1.0000
K2PI	37	-1959.7757	3993.5514	0.0000	1.0000
SYM	40	-1966.5223	4013.0446	0.0000	1.0000
K2P	36	-1974.7250	4021.4501	0.0000	1.0000
F81G	39	-1999.9672	4077.9345	0.0000	1.0000
F81IG	40	-1999.9670	4079.9341	0.0000	1.0000
F81I	39	-2001.2877	4080.5754	0.0000	1.0000
JC69G	36	-2016.4631	4104.9261	0.0000	1.0000
F81	38	-2015.5610	4107.1220	0.0000	1.0000
JC69IG	37	-2018.0368	4110.0736	0.0000	1.0000
JC69I	36	-2019.2268	4110.4536	0.0000	1.0000
JC69	35	-2031.5896	4133.1792	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1936.3394	4128.6225	0.8563	0.8563
HKYI	40	-1938.4375	4132.8188	0.1051	0.9614
HKYIG	41	-1936.3380	4135.0183	0.0350	0.9964
GTRG	44	-1929.1892	4139.9166	0.0030	0.9994
GTRI	44	-1931.0247	4143.5876	0.0005	0.9999
GTRIG	45	-1929.1945	4146.3258	0.0001	1.0000
K2PG	37	-1957.9396	4152.6273	0.0000	1.0000
K2PI	37	-1959.7757	4156.2995	0.0000	1.0000
HKY	39	-1953.4795	4156.5042	0.0000	1.0000
K2PIG	38	-1957.9374	4159.0215	0.0000	1.0000
SYMG	41	-1950.7416	4163.8256	0.0000	1.0000
GTR	43	-1944.9713	4165.0822	0.0000	1.0000
SYMI	41	-1952.4035	4167.1494	0.0000	1.0000
SYMIG	42	-1950.7413	4170.2236	0.0000	1.0000
K2P	36	-1974.7250	4179.7995	0.0000	1.0000
SYM	40	-1966.5223	4188.9884	0.0000	1.0000
F81G	39	-1999.9672	4249.4797	0.0000	1.0000
F81I	39	-2001.2877	4252.1206	0.0000	1.0000
F81IG	40	-1999.9670	4255.8779	0.0000	1.0000
JC69G	36	-2016.4631	4263.2755	0.0000	1.0000
JC69I	36	-2019.2268	4268.8030	0.0000	1.0000
JC69IG	37	-2018.0368	4272.8216	0.0000	1.0000
F81	38	-2015.5610	4274.2686	0.0000	1.0000
JC69	35	-2031.5896	4287.1300	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/chr11_6481.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6481.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/chr11_6481.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6481.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/chr11_6481.phylip = 1 - 601;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_6481.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

