
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:18 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_7691.phylip" (19 taxa, 803 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	-2084.9220	4263.0683	0.5584	0.5584
GTRIG	45	-2084.5377	4264.5444	0.2669	0.8253
GTRI	44	-2086.1975	4265.6194	0.1559	0.9812
HKYG	40	-2093.3949	4271.0944	0.0101	0.9913
HKYIG	41	-2092.9514	4272.4284	0.0052	0.9965
HKYI	40	-2094.4583	4273.2211	0.0035	1.0000
GTR	43	-2104.5192	4300.0240	0.0000	1.0000
HKY	39	-2114.1885	4310.4660	0.0000	1.0000
F81G	39	-2120.5017	4323.0924	0.0000	1.0000
K2PG	37	-2122.7644	4323.2046	0.0000	1.0000
K2PIG	38	-2122.2319	4324.3433	0.0000	1.0000
F81IG	40	-2120.0568	4324.4182	0.0000	1.0000
SYMG	41	-2119.2699	4325.0655	0.0000	1.0000
K2PI	37	-2123.7274	4325.1305	0.0000	1.0000
F81I	39	-2121.5328	4325.1546	0.0000	1.0000
SYMIG	42	-2118.8247	4326.4021	0.0000	1.0000
SYMI	41	-2120.2873	4327.1002	0.0000	1.0000
F81	38	-2141.2509	4362.3814	0.0000	1.0000
SYM	40	-2140.0339	4364.3722	0.0000	1.0000
K2P	36	-2145.0223	4365.5225	0.0000	1.0000
JC69G	36	-2147.7866	4371.0510	0.0000	1.0000
JC69IG	37	-2147.3141	4372.3040	0.0000	1.0000
JC69I	36	-2148.7521	4372.9821	0.0000	1.0000
JC69	35	-2169.2879	4411.8613	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2084.9220	4257.8441	0.5430	0.5430
GTRIG	45	-2084.5377	4259.0754	0.2934	0.8364
GTRI	44	-2086.1975	4260.3951	0.1517	0.9881
HKYG	40	-2093.3949	4266.7899	0.0062	0.9943
HKYIG	41	-2092.9514	4267.9027	0.0036	0.9979
HKYI	40	-2094.4583	4268.9166	0.0021	1.0000
GTR	43	-2104.5192	4295.0385	0.0000	1.0000
HKY	39	-2114.1885	4306.3769	0.0000	1.0000
F81G	39	-2120.5017	4319.0033	0.0000	1.0000
K2PG	37	-2122.7644	4319.5288	0.0000	1.0000
F81IG	40	-2120.0568	4320.1137	0.0000	1.0000
K2PIG	38	-2122.2319	4320.4637	0.0000	1.0000
SYMG	41	-2119.2699	4320.5398	0.0000	1.0000
F81I	39	-2121.5328	4321.0655	0.0000	1.0000
K2PI	37	-2123.7274	4321.4547	0.0000	1.0000
SYMIG	42	-2118.8247	4321.6495	0.0000	1.0000
SYMI	41	-2120.2873	4322.5745	0.0000	1.0000
F81	38	-2141.2509	4358.5018	0.0000	1.0000
SYM	40	-2140.0339	4360.0677	0.0000	1.0000
K2P	36	-2145.0223	4362.0447	0.0000	1.0000
JC69G	36	-2147.7866	4367.5732	0.0000	1.0000
JC69IG	37	-2147.3141	4368.6282	0.0000	1.0000
JC69I	36	-2148.7521	4369.5043	0.0000	1.0000
JC69	35	-2169.2879	4408.5758	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2093.3949	4454.3241	0.7091	0.7091
HKYI	40	-2094.4583	4456.4508	0.2449	0.9540
HKYIG	41	-2092.9514	4460.1253	0.0390	0.9930
GTRG	44	-2084.9220	4464.1317	0.0053	0.9983
GTRI	44	-2086.1975	4466.6827	0.0015	0.9997
GTRIG	45	-2084.5377	4470.0514	0.0003	1.0000
HKY	39	-2114.1885	4489.2227	0.0000	1.0000
K2PG	37	-2122.7644	4492.9979	0.0000	1.0000
K2PI	37	-2123.7274	4494.9238	0.0000	1.0000
GTR	43	-2104.5192	4496.6377	0.0000	1.0000
K2PIG	38	-2122.2319	4498.6212	0.0000	1.0000
F81G	39	-2120.5017	4501.8492	0.0000	1.0000
F81I	39	-2121.5328	4503.9114	0.0000	1.0000
F81IG	40	-2120.0568	4507.6479	0.0000	1.0000
SYMG	41	-2119.2699	4512.7624	0.0000	1.0000
SYMI	41	-2120.2873	4514.7971	0.0000	1.0000
SYMIG	42	-2118.8247	4518.5604	0.0000	1.0000
K2P	36	-2145.0223	4530.8254	0.0000	1.0000
JC69G	36	-2147.7866	4536.3539	0.0000	1.0000
F81	38	-2141.2509	4536.6593	0.0000	1.0000
JC69I	36	-2148.7521	4538.2851	0.0000	1.0000
JC69IG	37	-2147.3141	4542.0973	0.0000	1.0000
SYM	40	-2140.0339	4547.6019	0.0000	1.0000
JC69	35	-2169.2879	4572.6682	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_7691.phylip = 1 - 803;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7691.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_7691.phylip = 1 - 803;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7691.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/chrZ_7691.phylip = 1 - 803;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7691.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

