
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:20 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/chrZ_4841.phylip" (19 taxa, 348 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2P


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	-951.4787	2004.0267	0.3155	0.3155
HKYG	40	-957.1422	2004.9684	0.1970	0.5125
GTRI	44	-952.2131	2005.4954	0.1514	0.6639
HKYI	40	-957.9844	2006.6529	0.0849	0.7487
GTRIG	45	-951.4841	2006.6769	0.0838	0.8326
HKY	39	-959.6675	2007.4649	0.0565	0.8891
HKYIG	41	-957.1421	2007.5390	0.0545	0.9436
GTR	43	-954.6170	2007.6814	0.0507	0.9943
K2PG	37	-965.5131	2014.0972	0.0021	0.9964
K2PI	37	-966.4140	2015.8991	0.0008	0.9972
F81G	39	-964.2325	2016.5948	0.0006	0.9978
K2PIG	38	-965.5128	2016.6179	0.0006	0.9984
K2P	36	-968.0528	2016.6715	0.0006	0.9990
F81I	39	-965.0606	2018.2511	0.0003	0.9992
SYMG	41	-962.6913	2018.6376	0.0002	0.9994
F81	38	-966.6939	2018.9800	0.0002	0.9996
F81IG	40	-964.2323	2019.1486	0.0002	0.9998
SYMI	41	-963.5558	2020.3665	0.0001	0.9999
SYMIG	42	-962.6911	2021.2249	0.0001	0.9999
SYM	40	-965.3730	2021.4301	0.0001	1.0000
JC69G	36	-971.5659	2023.6977	0.0000	1.0000
JC69I	36	-972.4366	2025.4392	0.0000	1.0000
JC69	35	-974.0435	2026.1639	0.0000	1.0000
JC69IG	37	-971.5656	2026.2022	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-951.4787	1990.9574	0.4258	0.4258
GTRI	44	-952.2131	1992.4261	0.2043	0.6300
GTRIG	45	-951.4841	1992.9683	0.1558	0.7858
HKYG	40	-957.1422	1994.2844	0.0807	0.8665
GTR	43	-954.6170	1995.2340	0.0502	0.9167
HKYI	40	-957.9844	1995.9689	0.0347	0.9514
HKYIG	41	-957.1421	1996.2841	0.0297	0.9811
HKY	39	-959.6675	1997.3350	0.0176	0.9986
K2PG	37	-965.5131	2005.0262	0.0004	0.9990
F81G	39	-964.2325	2006.4649	0.0002	0.9992
K2PI	37	-966.4140	2006.8281	0.0002	0.9994
K2PIG	38	-965.5128	2007.0256	0.0001	0.9995
SYMG	41	-962.6913	2007.3827	0.0001	0.9996
K2P	36	-968.0528	2008.1056	0.0001	0.9997
F81I	39	-965.0606	2008.1212	0.0001	0.9998
F81IG	40	-964.2323	2008.4645	0.0001	0.9998
SYMI	41	-963.5558	2009.1116	0.0000	0.9999
SYMIG	42	-962.6911	2009.3823	0.0000	0.9999
F81	38	-966.6939	2009.3877	0.0000	1.0000
SYM	40	-965.3730	2010.7461	0.0000	1.0000
JC69G	36	-971.5659	2015.1318	0.0000	1.0000
JC69I	36	-972.4366	2016.8733	0.0000	1.0000
JC69IG	37	-971.5656	2017.1312	0.0000	1.0000
JC69	35	-974.0435	2018.0869	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-968.0528	2146.7849	0.2896	0.2896
K2PG	37	-965.5131	2147.5577	0.1968	0.4864
HKY	39	-959.6675	2147.5709	0.1955	0.6819
HKYG	40	-957.1422	2148.3725	0.1309	0.8128
K2PI	37	-966.4140	2149.3596	0.0799	0.8927
HKYI	40	-957.9844	2150.0570	0.0564	0.9491
JC69	35	-974.0435	2152.9140	0.0135	0.9626
K2PIG	38	-965.5128	2153.4093	0.0106	0.9732
JC69G	36	-971.5659	2153.8111	0.0086	0.9818
HKYIG	41	-957.1421	2154.2244	0.0070	0.9888
JC69I	36	-972.4366	2155.5526	0.0036	0.9925
F81	38	-966.6939	2155.7714	0.0032	0.9957
F81G	39	-964.2325	2156.7008	0.0020	0.9977
F81I	39	-965.0606	2158.3571	0.0009	0.9986
JC69IG	37	-971.5656	2159.6627	0.0005	0.9991
GTRG	44	-951.4787	2160.4543	0.0003	0.9994
GTR	43	-954.6170	2160.8787	0.0003	0.9996
GTRI	44	-952.2131	2161.9230	0.0001	0.9998
F81IG	40	-964.2323	2162.5526	0.0001	0.9999
SYM	40	-965.3730	2164.8342	0.0000	0.9999
SYMG	41	-962.6913	2165.3230	0.0000	1.0000
GTRIG	45	-951.4841	2166.3174	0.0000	1.0000
SYMI	41	-963.5558	2167.0519	0.0000	1.0000
SYMIG	42	-962.6911	2171.1748	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/chrZ_4841.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4841.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/chrZ_4841.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4841.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 (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4841.phylip = 1 - 348;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4841.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

