
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:46 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/chr7_10555.phylip" (19 taxa, 868 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: K2PG


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	-2418.0586	4928.9288	0.7242	0.7242
GTRG	44	-2419.2980	4931.4077	0.2097	0.9338
GTRIG	45	-2419.5161	4934.0688	0.0554	0.9893
HKYG	40	-2428.0203	4940.0068	0.0028	0.9921
SYMI	41	-2427.1267	4940.4229	0.0023	0.9944
SYMIG	42	-2426.0364	4940.4509	0.0023	0.9967
HKYIG	41	-2427.5408	4941.2511	0.0015	0.9982
HKYI	40	-2428.7133	4941.3928	0.0014	0.9997
SYMG	41	-2429.0871	4944.3437	0.0003	1.0000
K2PG	37	-2437.3055	4951.9990	0.0000	1.0000
K2PIG	38	-2436.5249	4952.6251	0.0000	1.0000
K2PI	37	-2439.0451	4955.4781	0.0000	1.0000
F81G	39	-2461.4571	5004.6823	0.0000	1.0000
F81I	39	-2463.2387	5008.2455	0.0000	1.0000
F81IG	40	-2462.2504	5008.4670	0.0000	1.0000
JC69G	36	-2468.9418	5013.0895	0.0000	1.0000
GTR	43	-2461.2755	5013.1433	0.0000	1.0000
JC69I	36	-2470.6164	5016.4385	0.0000	1.0000
JC69IG	37	-2469.7474	5016.8829	0.0000	1.0000
HKY	39	-2467.6404	5017.0490	0.0000	1.0000
SYM	40	-2468.7825	5021.5312	0.0000	1.0000
K2P	36	-2475.7379	5026.6817	0.0000	1.0000
F81	38	-2496.8527	5073.2807	0.0000	1.0000
JC69	35	-2503.7499	5080.5287	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2418.0586	4924.1171	0.7216	0.7216
GTRG	44	-2419.2980	4926.5960	0.2089	0.9306
GTRIG	45	-2419.5161	4929.0323	0.0618	0.9924
HKYG	40	-2428.0203	4936.0407	0.0019	0.9942
SYMIG	42	-2426.0364	4936.0727	0.0018	0.9961
SYMI	41	-2427.1267	4936.2534	0.0017	0.9977
HKYIG	41	-2427.5408	4937.0816	0.0011	0.9988
HKYI	40	-2428.7133	4937.4266	0.0009	0.9998
SYMG	41	-2429.0871	4940.1742	0.0002	1.0000
K2PG	37	-2437.3055	4948.6110	0.0000	1.0000
K2PIG	38	-2436.5249	4949.0497	0.0000	1.0000
K2PI	37	-2439.0451	4952.0901	0.0000	1.0000
F81G	39	-2461.4571	5000.9142	0.0000	1.0000
F81I	39	-2463.2387	5004.4774	0.0000	1.0000
F81IG	40	-2462.2504	5004.5008	0.0000	1.0000
GTR	43	-2461.2755	5008.5510	0.0000	1.0000
JC69G	36	-2468.9418	5009.8837	0.0000	1.0000
JC69I	36	-2470.6164	5013.2327	0.0000	1.0000
HKY	39	-2467.6404	5013.2809	0.0000	1.0000
JC69IG	37	-2469.7474	5013.4949	0.0000	1.0000
SYM	40	-2468.7825	5017.5651	0.0000	1.0000
K2P	36	-2475.7379	5023.4759	0.0000	1.0000
F81	38	-2496.8527	5069.7053	0.0000	1.0000
JC69	35	-2503.7499	5077.4999	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2437.3055	5124.9601	0.5092	0.5092
HKYG	40	-2428.0203	5126.6884	0.2146	0.7238
HKYI	40	-2428.7133	5128.0743	0.1073	0.8311
K2PI	37	-2439.0451	5128.4392	0.0894	0.9206
K2PIG	38	-2436.5249	5130.1650	0.0377	0.9583
SYMI	41	-2427.1267	5131.6673	0.0178	0.9761
HKYIG	41	-2427.5408	5132.4955	0.0118	0.9879
GTRI	44	-2418.0586	5133.8296	0.0060	0.9939
SYMG	41	-2429.0871	5135.5880	0.0025	0.9964
SYMIG	42	-2426.0364	5136.2528	0.0018	0.9982
GTRG	44	-2419.2980	5136.3084	0.0017	1.0000
GTRIG	45	-2419.5161	5143.5109	0.0000	1.0000
JC69G	36	-2468.9418	5181.4666	0.0000	1.0000
JC69I	36	-2470.6164	5184.8156	0.0000	1.0000
F81G	39	-2461.4571	5186.7957	0.0000	1.0000
JC69IG	37	-2469.7474	5189.8440	0.0000	1.0000
F81I	39	-2463.2387	5190.3589	0.0000	1.0000
K2P	36	-2475.7379	5195.0588	0.0000	1.0000
F81IG	40	-2462.2504	5195.1485	0.0000	1.0000
HKY	39	-2467.6404	5199.1624	0.0000	1.0000
SYM	40	-2468.7825	5208.2127	0.0000	1.0000
GTR	43	-2461.2755	5213.4973	0.0000	1.0000
JC69	35	-2503.7499	5244.3166	0.0000	1.0000
F81	38	-2496.8527	5250.8206	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/chr7_10555.phylip = 1 - 868;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10555.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/chr7_10555.phylip = 1 - 868;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10555.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10555.phylip = 1 - 868;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10555.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

