
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:20 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/chr4_9240.phylip" (19 taxa, 650 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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
HKYI	40	-2039.0240	4163.4338	0.2679	0.2679
K2PI	37	-2042.4238	4163.4424	0.2668	0.5347
GTRI	44	-2034.7996	4164.1447	0.1878	0.7225
K2PIG	38	-2042.7910	4166.4331	0.0598	0.7823
K2PG	37	-2044.1998	4166.9944	0.0452	0.8275
HKYG	40	-2040.8044	4166.9947	0.0452	0.8726
GTRG	44	-2036.3164	4167.1783	0.0412	0.9138
HKYIG	41	-2040.0679	4167.8003	0.0302	0.9440
SYMI	41	-2040.1141	4167.8927	0.0288	0.9728
GTRIG	45	-2035.9781	4168.8105	0.0182	0.9911
SYMIG	42	-2040.7260	4171.4025	0.0050	0.9960
SYMG	41	-2042.1013	4171.8670	0.0040	1.0000
JC69I	36	-2067.0293	4210.4045	0.0000	1.0000
JC69G	36	-2067.5602	4211.4663	0.0000	1.0000
F81I	39	-2064.6705	4212.4557	0.0000	1.0000
F81G	39	-2065.2885	4213.6918	0.0000	1.0000
JC69IG	37	-2067.5601	4213.7149	0.0000	1.0000
F81IG	40	-2065.2884	4215.9627	0.0000	1.0000
K2P	36	-2084.8619	4246.0697	0.0000	1.0000
HKY	39	-2081.8400	4246.7947	0.0000	1.0000
GTR	43	-2079.3227	4250.8896	0.0000	1.0000
SYM	40	-2083.4736	4252.3330	0.0000	1.0000
JC69	35	-2108.2212	4290.5467	0.0000	1.0000
F81	38	-2105.8767	4292.6045	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2034.7996	4157.5992	0.3063	0.3063
HKYI	40	-2039.0240	4158.0479	0.2447	0.5510
K2PI	37	-2042.4238	4158.8476	0.1641	0.7151
GTRG	44	-2036.3164	4160.6329	0.0672	0.7823
K2PIG	38	-2042.7910	4161.5820	0.0418	0.8241
HKYG	40	-2040.8044	4161.6088	0.0413	0.8654
GTRIG	45	-2035.9781	4161.9562	0.0347	0.9001
HKYIG	41	-2040.0679	4162.1358	0.0317	0.9318
SYMI	41	-2040.1141	4162.2282	0.0303	0.9620
K2PG	37	-2044.1998	4162.3996	0.0278	0.9898
SYMIG	42	-2040.7260	4165.4519	0.0060	0.9959
SYMG	41	-2042.1013	4166.2026	0.0041	1.0000
JC69I	36	-2067.0293	4206.0586	0.0000	1.0000
JC69G	36	-2067.5602	4207.1204	0.0000	1.0000
F81I	39	-2064.6705	4207.3409	0.0000	1.0000
F81G	39	-2065.2885	4208.5770	0.0000	1.0000
JC69IG	37	-2067.5601	4209.1201	0.0000	1.0000
F81IG	40	-2065.2884	4210.5768	0.0000	1.0000
HKY	39	-2081.8400	4241.6800	0.0000	1.0000
K2P	36	-2084.8619	4241.7239	0.0000	1.0000
GTR	43	-2079.3227	4244.6454	0.0000	1.0000
SYM	40	-2083.4736	4246.9471	0.0000	1.0000
JC69	35	-2108.2212	4286.4425	0.0000	1.0000
F81	38	-2105.8767	4287.7535	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-2042.4238	4324.4956	0.8343	0.8343
K2PG	37	-2044.1998	4328.0476	0.1413	0.9755
K2PIG	38	-2042.7910	4331.7070	0.0227	0.9982
HKYI	40	-2039.0240	4337.1268	0.0015	0.9997
HKYG	40	-2040.8044	4340.6877	0.0003	1.0000
HKYIG	41	-2040.0679	4345.6916	0.0000	1.0000
SYMI	41	-2040.1141	4345.7840	0.0000	1.0000
SYMG	41	-2042.1013	4349.7584	0.0000	1.0000
SYMIG	42	-2040.7260	4353.4848	0.0000	1.0000
GTRI	44	-2034.7996	4354.5860	0.0000	1.0000
GTRG	44	-2036.3164	4357.6196	0.0000	1.0000
GTRIG	45	-2035.9781	4363.4199	0.0000	1.0000
JC69I	36	-2067.0293	4367.2296	0.0000	1.0000
JC69G	36	-2067.5602	4368.2914	0.0000	1.0000
JC69IG	37	-2067.5601	4374.7681	0.0000	1.0000
F81I	39	-2064.6705	4381.9429	0.0000	1.0000
F81G	39	-2065.2885	4383.1789	0.0000	1.0000
F81IG	40	-2065.2884	4389.6557	0.0000	1.0000
K2P	36	-2084.8619	4402.8949	0.0000	1.0000
HKY	39	-2081.8400	4416.2819	0.0000	1.0000
SYM	40	-2083.4736	4426.0260	0.0000	1.0000
GTR	43	-2079.3227	4437.1552	0.0000	1.0000
JC69	35	-2108.2212	4443.1365	0.0000	1.0000
F81	38	-2105.8767	4457.8784	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip = 1 - 650;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9240.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

