
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:16 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/chr11_2305.phylip" (19 taxa, 708 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	-2436.9048	4967.7825	0.6772	0.6772
GTRIG	45	-2436.9048	4970.0633	0.2165	0.8937
GTRI	44	-2438.7649	4971.5027	0.1054	0.9991
HKYG	40	-2448.3915	4981.7006	0.0006	0.9997
HKYIG	41	-2448.3950	4983.9613	0.0002	0.9999
HKYI	40	-2450.4808	4985.8792	0.0001	1.0000
SYMG	41	-2464.5652	5016.3017	0.0000	1.0000
SYMIG	42	-2464.5652	5018.5620	0.0000	1.0000
SYMI	41	-2466.6625	5020.4962	0.0000	1.0000
GTR	43	-2471.9270	5035.5528	0.0000	1.0000
K2PG	37	-2480.4809	5039.1589	0.0000	1.0000
K2PIG	38	-2480.4889	5041.4084	0.0000	1.0000
K2PI	37	-2483.0036	5044.2043	0.0000	1.0000
HKY	39	-2486.1809	5055.0325	0.0000	1.0000
F81G	39	-2495.1002	5072.8711	0.0000	1.0000
F81IG	40	-2495.1002	5075.1180	0.0000	1.0000
F81I	39	-2497.3655	5077.4017	0.0000	1.0000
SYM	40	-2499.9392	5084.7959	0.0000	1.0000
K2P	36	-2519.1250	5114.2201	0.0000	1.0000
F81	38	-2533.6748	5147.7800	0.0000	1.0000
JC69G	36	-2536.9280	5149.8263	0.0000	1.0000
JC69IG	37	-2536.9280	5152.0530	0.0000	1.0000
JC69I	36	-2538.6573	5153.2848	0.0000	1.0000
JC69	35	-2572.8175	5219.3849	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2436.9048	4961.8096	0.6560	0.6560
GTRIG	45	-2436.9048	4963.8095	0.2413	0.8973
GTRI	44	-2438.7649	4965.5298	0.1021	0.9995
HKYG	40	-2448.3915	4976.7831	0.0004	0.9998
HKYIG	41	-2448.3950	4978.7901	0.0001	1.0000
HKYI	40	-2450.4808	4980.9617	0.0000	1.0000
SYMG	41	-2464.5652	5011.1305	0.0000	1.0000
SYMIG	42	-2464.5652	5013.1304	0.0000	1.0000
SYMI	41	-2466.6625	5015.3250	0.0000	1.0000
GTR	43	-2471.9270	5029.8540	0.0000	1.0000
K2PG	37	-2480.4809	5034.9619	0.0000	1.0000
K2PIG	38	-2480.4889	5036.9779	0.0000	1.0000
K2PI	37	-2483.0036	5040.0072	0.0000	1.0000
HKY	39	-2486.1809	5050.3618	0.0000	1.0000
F81G	39	-2495.1002	5068.2005	0.0000	1.0000
F81IG	40	-2495.1002	5070.2005	0.0000	1.0000
F81I	39	-2497.3655	5072.7311	0.0000	1.0000
SYM	40	-2499.9392	5079.8784	0.0000	1.0000
K2P	36	-2519.1250	5110.2499	0.0000	1.0000
F81	38	-2533.6748	5143.3495	0.0000	1.0000
JC69G	36	-2536.9280	5145.8561	0.0000	1.0000
JC69IG	37	-2536.9280	5147.8559	0.0000	1.0000
JC69I	36	-2538.6573	5149.3146	0.0000	1.0000
JC69	35	-2572.8175	5215.6349	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2448.3915	5159.2808	0.7178	0.7178
GTRG	44	-2436.9048	5162.5572	0.1395	0.8573
HKYI	40	-2450.4808	5163.4594	0.0888	0.9462
HKYIG	41	-2448.3950	5165.8503	0.0269	0.9730
GTRI	44	-2438.7649	5166.2773	0.0217	0.9948
GTRIG	45	-2436.9048	5169.1195	0.0052	1.0000
SYMG	41	-2464.5652	5198.1907	0.0000	1.0000
SYMI	41	-2466.6625	5202.3852	0.0000	1.0000
K2PG	37	-2480.4809	5203.7723	0.0000	1.0000
SYMIG	42	-2464.5652	5204.7531	0.0000	1.0000
K2PI	37	-2483.0036	5208.8177	0.0000	1.0000
K2PIG	38	-2480.4889	5210.3507	0.0000	1.0000
GTR	43	-2471.9270	5226.0391	0.0000	1.0000
HKY	39	-2486.1809	5228.2971	0.0000	1.0000
F81G	39	-2495.1002	5246.1358	0.0000	1.0000
F81I	39	-2497.3655	5250.6664	0.0000	1.0000
F81IG	40	-2495.1002	5252.6983	0.0000	1.0000
SYM	40	-2499.9392	5262.3762	0.0000	1.0000
K2P	36	-2519.1250	5274.4979	0.0000	1.0000
JC69G	36	-2536.9280	5310.1040	0.0000	1.0000
JC69I	36	-2538.6573	5313.5626	0.0000	1.0000
JC69IG	37	-2536.9280	5316.6664	0.0000	1.0000
F81	38	-2533.6748	5316.7224	0.0000	1.0000
JC69	35	-2572.8175	5375.3205	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/chr11_2305.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_2305.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/chr11_2305.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_2305.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/chr11_2305.phylip = 1 - 708;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_2305.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

