
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:47 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/chr5_10252.phylip" (19 taxa, 496 characters)

Minimum AIC  model: GTRG
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	-1952.7150	3992.6389	0.4160	0.4160
GTRG	44	-1948.5141	3993.8087	0.2318	0.6478
HKYIG	41	-1952.1672	3993.9204	0.2192	0.8670
GTRIG	45	-1947.9742	3995.1485	0.1186	0.9856
HKYI	40	-1956.4402	4000.0891	0.0100	0.9957
GTRI	44	-1952.9768	4002.7340	0.0027	0.9983
K2PG	37	-1962.2600	4004.6597	0.0010	0.9994
K2PIG	38	-1961.6839	4005.8535	0.0006	0.9999
SYMG	41	-1960.8914	4011.3688	0.0000	1.0000
K2PI	37	-1965.9720	4012.0838	0.0000	1.0000
SYMIG	42	-1960.3340	4012.6414	0.0000	1.0000
SYMI	41	-1964.7348	4019.0555	0.0000	1.0000
HKY	39	-2007.4002	4099.6425	0.0000	1.0000
F81G	39	-2007.5010	4099.8440	0.0000	1.0000
F81IG	40	-2006.8867	4100.9823	0.0000	1.0000
GTR	43	-2004.2148	4102.8012	0.0000	1.0000
F81I	39	-2010.5513	4105.9447	0.0000	1.0000
JC69G	36	-2014.1461	4106.0960	0.0000	1.0000
JC69IG	37	-2013.7195	4107.5786	0.0000	1.0000
K2P	36	-2016.2777	4110.3593	0.0000	1.0000
JC69I	36	-2017.3072	4112.4183	0.0000	1.0000
SYM	40	-2014.9229	4117.0546	0.0000	1.0000
F81	38	-2059.1750	4200.8358	0.0000	1.0000
JC69	35	-2065.9774	4207.4331	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1948.5141	3985.0282	0.3330	0.3330
HKYG	40	-1952.7150	3985.4301	0.2724	0.6054
GTRIG	45	-1947.9742	3985.9485	0.2102	0.8156
HKYIG	41	-1952.1672	3986.3345	0.1733	0.9889
HKYI	40	-1956.4402	3992.8803	0.0066	0.9955
GTRI	44	-1952.9768	3993.9536	0.0038	0.9993
K2PG	37	-1962.2600	3998.5200	0.0004	0.9997
K2PIG	38	-1961.6839	3999.3678	0.0003	0.9999
SYMG	41	-1960.8914	4003.7829	0.0000	1.0000
SYMIG	42	-1960.3340	4004.6679	0.0000	1.0000
K2PI	37	-1965.9720	4005.9440	0.0000	1.0000
SYMI	41	-1964.7348	4011.4696	0.0000	1.0000
HKY	39	-2007.4002	4092.8004	0.0000	1.0000
F81G	39	-2007.5010	4093.0019	0.0000	1.0000
F81IG	40	-2006.8867	4093.7735	0.0000	1.0000
GTR	43	-2004.2148	4094.4296	0.0000	1.0000
F81I	39	-2010.5513	4099.1026	0.0000	1.0000
JC69G	36	-2014.1461	4100.2921	0.0000	1.0000
JC69IG	37	-2013.7195	4101.4389	0.0000	1.0000
K2P	36	-2016.2777	4104.5553	0.0000	1.0000
JC69I	36	-2017.3072	4106.6144	0.0000	1.0000
SYM	40	-2014.9229	4109.8458	0.0000	1.0000
F81	38	-2059.1750	4194.3501	0.0000	1.0000
JC69	35	-2065.9774	4201.9548	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1952.7150	4153.6931	0.5063	0.5063
K2PG	37	-1962.2600	4154.1633	0.4002	0.9066
HKYIG	41	-1952.1672	4158.8041	0.0393	0.9459
K2PIG	38	-1961.6839	4159.2176	0.0320	0.9779
HKYI	40	-1956.4402	4161.1434	0.0122	0.9901
K2PI	37	-1965.9720	4161.5873	0.0098	0.9998
GTRG	44	-1948.5141	4170.1176	0.0001	1.0000
GTRIG	45	-1947.9742	4175.2444	0.0000	1.0000
SYMG	41	-1960.8914	4176.2525	0.0000	1.0000
GTRI	44	-1952.9768	4179.0429	0.0000	1.0000
SYMIG	42	-1960.3340	4181.3441	0.0000	1.0000
SYMI	41	-1964.7348	4183.9392	0.0000	1.0000
JC69G	36	-2014.1461	4251.7289	0.0000	1.0000
K2P	36	-2016.2777	4255.9921	0.0000	1.0000
HKY	39	-2007.4002	4256.8569	0.0000	1.0000
F81G	39	-2007.5010	4257.0584	0.0000	1.0000
JC69IG	37	-2013.7195	4257.0822	0.0000	1.0000
JC69I	36	-2017.3072	4258.0511	0.0000	1.0000
F81IG	40	-2006.8867	4262.0365	0.0000	1.0000
F81I	39	-2010.5513	4263.1591	0.0000	1.0000
GTR	43	-2004.2148	4275.3123	0.0000	1.0000
SYM	40	-2014.9229	4278.1088	0.0000	1.0000
JC69	35	-2065.9774	4349.1850	0.0000	1.0000
F81	38	-2059.1750	4354.1999	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/chr5_10252.phylip = 1 - 496;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10252.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10252.phylip = 1 - 496;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10252.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/chr5_10252.phylip = 1 - 496;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10252.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

