
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:22 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_11169.phylip" (19 taxa, 711 characters)

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


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
GTRI	44	-2098.2429	4290.4317	0.4463	0.4463
GTRG	44	-2098.3085	4290.5629	0.4180	0.8643
GTRIG	45	-2098.3085	4292.8426	0.1337	0.9980
HKYI	40	-2108.9135	4302.7226	0.0010	0.9990
HKYG	40	-2109.1214	4303.1383	0.0008	0.9997
HKYIG	41	-2109.1213	4305.3907	0.0003	1.0000
K2PI	37	-2135.5858	4349.3499	0.0000	1.0000
K2PG	37	-2135.6642	4349.5068	0.0000	1.0000
SYMI	41	-2132.0417	4351.2313	0.0000	1.0000
SYMG	41	-2132.1236	4351.3952	0.0000	1.0000
K2PIG	38	-2135.6643	4351.7392	0.0000	1.0000
SYMIG	42	-2132.1237	4353.6545	0.0000	1.0000
GTR	43	-2138.0583	4367.7897	0.0000	1.0000
HKY	39	-2146.4752	4375.6001	0.0000	1.0000
F81I	39	-2156.3281	4395.3060	0.0000	1.0000
F81G	39	-2156.6823	4396.0143	0.0000	1.0000
F81IG	40	-2156.6823	4398.2602	0.0000	1.0000
K2P	36	-2171.9184	4419.7894	0.0000	1.0000
SYM	40	-2168.3743	4421.6441	0.0000	1.0000
JC69I	36	-2177.1626	4430.2777	0.0000	1.0000
JC69G	36	-2177.4434	4430.8393	0.0000	1.0000
JC69IG	37	-2177.4434	4433.0651	0.0000	1.0000
F81	38	-2194.1277	4468.6661	0.0000	1.0000
JC69	35	-2214.3581	4502.4496	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2098.2429	4284.4857	0.4379	0.4379
GTRG	44	-2098.3085	4284.6170	0.4101	0.8480
GTRIG	45	-2098.3085	4286.6171	0.1509	0.9988
HKYI	40	-2108.9135	4297.8271	0.0006	0.9994
HKYG	40	-2109.1214	4298.2428	0.0005	0.9998
HKYIG	41	-2109.1213	4300.2427	0.0002	1.0000
K2PI	37	-2135.5858	4345.1716	0.0000	1.0000
K2PG	37	-2135.6642	4345.3285	0.0000	1.0000
SYMI	41	-2132.0417	4346.0833	0.0000	1.0000
SYMG	41	-2132.1236	4346.2473	0.0000	1.0000
K2PIG	38	-2135.6643	4347.3285	0.0000	1.0000
SYMIG	42	-2132.1237	4348.2474	0.0000	1.0000
GTR	43	-2138.0583	4362.1166	0.0000	1.0000
HKY	39	-2146.4752	4370.9503	0.0000	1.0000
F81I	39	-2156.3281	4390.6562	0.0000	1.0000
F81G	39	-2156.6823	4391.3645	0.0000	1.0000
F81IG	40	-2156.6823	4393.3647	0.0000	1.0000
K2P	36	-2171.9184	4415.8369	0.0000	1.0000
SYM	40	-2168.3743	4416.7486	0.0000	1.0000
JC69I	36	-2177.1626	4426.3252	0.0000	1.0000
JC69G	36	-2177.4434	4426.8868	0.0000	1.0000
JC69IG	37	-2177.4434	4428.8868	0.0000	1.0000
F81	38	-2194.1277	4464.2554	0.0000	1.0000
JC69	35	-2214.3581	4498.7162	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2108.9135	4480.4940	0.4973	0.4973
HKYG	40	-2109.1214	4480.9097	0.4040	0.9013
GTRI	44	-2098.2429	4485.4193	0.0424	0.9437
GTRG	44	-2098.3085	4485.5505	0.0397	0.9834
HKYIG	41	-2109.1213	4487.4763	0.0152	0.9985
GTRIG	45	-2098.3085	4492.1173	0.0015	1.0000
K2PI	37	-2135.5858	4514.1385	0.0000	1.0000
K2PG	37	-2135.6642	4514.2954	0.0000	1.0000
K2PIG	38	-2135.6643	4520.8621	0.0000	1.0000
SYMI	41	-2132.0417	4533.3169	0.0000	1.0000
SYMG	41	-2132.1236	4533.4808	0.0000	1.0000
SYMIG	42	-2132.1237	4540.0476	0.0000	1.0000
HKY	39	-2146.4752	4549.0506	0.0000	1.0000
GTR	43	-2138.0583	4558.4835	0.0000	1.0000
F81I	39	-2156.3281	4568.7565	0.0000	1.0000
F81G	39	-2156.6823	4569.4647	0.0000	1.0000
F81IG	40	-2156.6823	4576.0316	0.0000	1.0000
K2P	36	-2171.9184	4580.2371	0.0000	1.0000
JC69I	36	-2177.1626	4590.7254	0.0000	1.0000
JC69G	36	-2177.4434	4591.2870	0.0000	1.0000
JC69IG	37	-2177.4434	4597.8537	0.0000	1.0000
SYM	40	-2168.3743	4599.4155	0.0000	1.0000
F81	38	-2194.1277	4637.7890	0.0000	1.0000
JC69	35	-2214.3581	4658.5498	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/chr5_11169.phylip = 1 - 711;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11169.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 (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11169.phylip = 1 - 711;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11169.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 BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11169.phylip = 1 - 711;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_11169.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;


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End of Output

