
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:42 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/chr2_24910.phylip" (19 taxa, 616 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	-2020.0779	4135.0909	0.3150	0.3150
HKYG	40	-2024.8762	4135.4568	0.2623	0.5773
GTRI	44	-2021.0701	4137.0754	0.1168	0.6940
GTRIG	45	-2019.9489	4137.1609	0.1119	0.8059
HKYI	40	-2025.7981	4137.3005	0.1043	0.9103
HKYIG	41	-2024.8010	4137.6021	0.0897	1.0000
K2PG	37	-2048.4999	4175.8649	0.0000	1.0000
K2PI	37	-2049.3878	4177.6407	0.0000	1.0000
K2PIG	38	-2048.4564	4178.0496	0.0000	1.0000
HKY	39	-2047.9418	4179.3002	0.0000	1.0000
GTR	43	-2043.9383	4180.4919	0.0000	1.0000
SYMG	41	-2047.9159	4183.8317	0.0000	1.0000
SYMI	41	-2048.7566	4185.5132	0.0000	1.0000
SYMIG	42	-2047.8651	4186.0339	0.0000	1.0000
F81G	39	-2061.7246	4206.8659	0.0000	1.0000
F81IG	40	-2061.6702	4209.0448	0.0000	1.0000
F81I	39	-2063.6507	4210.7181	0.0000	1.0000
K2P	36	-2070.8261	4218.2533	0.0000	1.0000
SYM	40	-2070.0963	4225.8969	0.0000	1.0000
JC69G	36	-2081.3320	4239.2650	0.0000	1.0000
JC69I	36	-2082.0640	4240.7291	0.0000	1.0000
JC69IG	37	-2081.3040	4241.4731	0.0000	1.0000
F81	38	-2083.7225	4248.5820	0.0000	1.0000
JC69	35	-2103.0282	4280.4013	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2020.0779	4128.1557	0.3851	0.3851
HKYG	40	-2024.8762	4129.7524	0.1733	0.5584
GTRIG	45	-2019.9489	4129.8978	0.1612	0.7196
GTRI	44	-2021.0701	4130.1402	0.1428	0.8623
HKYI	40	-2025.7981	4131.5962	0.0689	0.9313
HKYIG	41	-2024.8010	4131.6021	0.0687	1.0000
K2PG	37	-2048.4999	4170.9998	0.0000	1.0000
K2PI	37	-2049.3878	4172.7757	0.0000	1.0000
K2PIG	38	-2048.4564	4172.9127	0.0000	1.0000
GTR	43	-2043.9383	4173.8766	0.0000	1.0000
HKY	39	-2047.9418	4173.8835	0.0000	1.0000
SYMG	41	-2047.9159	4177.8317	0.0000	1.0000
SYMI	41	-2048.7566	4179.5132	0.0000	1.0000
SYMIG	42	-2047.8651	4179.7302	0.0000	1.0000
F81G	39	-2061.7246	4201.4493	0.0000	1.0000
F81IG	40	-2061.6702	4203.3405	0.0000	1.0000
F81I	39	-2063.6507	4205.3015	0.0000	1.0000
K2P	36	-2070.8261	4213.6523	0.0000	1.0000
SYM	40	-2070.0963	4220.1926	0.0000	1.0000
JC69G	36	-2081.3320	4234.6640	0.0000	1.0000
JC69I	36	-2082.0640	4236.1280	0.0000	1.0000
JC69IG	37	-2081.3040	4236.6080	0.0000	1.0000
F81	38	-2083.7225	4243.4450	0.0000	1.0000
JC69	35	-2103.0282	4276.0564	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2024.8762	4306.6823	0.6936	0.6936
HKYI	40	-2025.7981	4308.5261	0.2759	0.9696
HKYIG	41	-2024.8010	4312.9552	0.0301	0.9997
GTRG	44	-2020.0779	4322.7786	0.0002	0.9999
GTRI	44	-2021.0701	4324.7630	0.0001	1.0000
GTRIG	45	-2019.9489	4328.9439	0.0000	1.0000
K2PG	37	-2048.4999	4334.6599	0.0000	1.0000
K2PI	37	-2049.3878	4336.4358	0.0000	1.0000
K2PIG	38	-2048.4564	4340.9961	0.0000	1.0000
HKY	39	-2047.9418	4346.3902	0.0000	1.0000
SYMG	41	-2047.9159	4359.1848	0.0000	1.0000
SYMI	41	-2048.7566	4360.8664	0.0000	1.0000
GTR	43	-2043.9383	4364.0762	0.0000	1.0000
SYMIG	42	-2047.8651	4365.5066	0.0000	1.0000
K2P	36	-2070.8261	4372.8892	0.0000	1.0000
F81G	39	-2061.7246	4373.9559	0.0000	1.0000
F81I	39	-2063.6507	4377.8081	0.0000	1.0000
F81IG	40	-2061.6702	4380.2703	0.0000	1.0000
JC69G	36	-2081.3320	4393.9009	0.0000	1.0000
JC69I	36	-2082.0640	4395.3649	0.0000	1.0000
SYM	40	-2070.0963	4397.1225	0.0000	1.0000
JC69IG	37	-2081.3040	4400.2682	0.0000	1.0000
F81	38	-2083.7225	4411.5284	0.0000	1.0000
JC69	35	-2103.0282	4430.8701	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/chr2_24910.phylip = 1 - 616;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24910.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/chr2_24910.phylip = 1 - 616;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24910.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/chr2_24910.phylip = 1 - 616;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_24910.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;


-------------------------------------------------------------
End of Output

