
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:58 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_10860.phylip" (19 taxa, 753 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	-2395.9120	4885.4173	0.5657	0.5657
GTRI	44	-2396.8199	4887.2330	0.2282	0.7939
GTRIG	45	-2395.9119	4887.6795	0.1825	0.9764
HKYG	40	-2404.1885	4892.9837	0.0129	0.9893
HKYI	40	-2404.8520	4894.3108	0.0066	0.9959
HKYIG	41	-2404.2239	4895.2917	0.0041	1.0000
GTR	43	-2431.4486	4954.2343	0.0000	1.0000
K2PG	37	-2441.1545	4960.2418	0.0000	1.0000
K2PI	37	-2441.2861	4960.5051	0.0000	1.0000
K2PIG	38	-2441.1679	4962.4870	0.0000	1.0000
HKY	39	-2442.2631	4966.9022	0.0000	1.0000
SYMG	41	-2440.2351	4967.3140	0.0000	1.0000
SYMI	41	-2440.4106	4967.6650	0.0000	1.0000
SYMIG	42	-2440.2348	4969.5570	0.0000	1.0000
F81G	39	-2477.5197	5037.4152	0.0000	1.0000
F81I	39	-2477.5584	5037.4926	0.0000	1.0000
F81IG	40	-2477.6629	5039.9325	0.0000	1.0000
K2P	36	-2482.6837	5041.0881	0.0000	1.0000
SYM	40	-2480.3163	5045.2393	0.0000	1.0000
JC69G	36	-2508.5192	5092.7592	0.0000	1.0000
JC69I	36	-2508.5244	5092.7695	0.0000	1.0000
JC69IG	37	-2508.5191	5094.9710	0.0000	1.0000
F81	38	-2515.0972	5110.3456	0.0000	1.0000
JC69	35	-2548.0537	5169.6220	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2395.9120	4879.8241	0.5564	0.5564
GTRI	44	-2396.8199	4881.6398	0.2244	0.7808
GTRIG	45	-2395.9119	4881.8238	0.2047	0.9855
HKYG	40	-2404.1885	4888.3769	0.0077	0.9933
HKYI	40	-2404.8520	4889.7040	0.0040	0.9973
HKYIG	41	-2404.2239	4890.4478	0.0027	1.0000
GTR	43	-2431.4486	4948.8972	0.0000	1.0000
K2PG	37	-2441.1545	4956.3089	0.0000	1.0000
K2PI	37	-2441.2861	4956.5722	0.0000	1.0000
K2PIG	38	-2441.1679	4958.3358	0.0000	1.0000
SYMG	41	-2440.2351	4962.4701	0.0000	1.0000
HKY	39	-2442.2631	4962.5263	0.0000	1.0000
SYMI	41	-2440.4106	4962.8211	0.0000	1.0000
SYMIG	42	-2440.2348	4964.4697	0.0000	1.0000
F81G	39	-2477.5197	5033.0393	0.0000	1.0000
F81I	39	-2477.5584	5033.1167	0.0000	1.0000
F81IG	40	-2477.6629	5035.3258	0.0000	1.0000
K2P	36	-2482.6837	5037.3675	0.0000	1.0000
SYM	40	-2480.3163	5040.6326	0.0000	1.0000
JC69G	36	-2508.5192	5089.0385	0.0000	1.0000
JC69I	36	-2508.5244	5089.0488	0.0000	1.0000
JC69IG	37	-2508.5191	5091.0381	0.0000	1.0000
F81	38	-2515.0972	5106.1944	0.0000	1.0000
JC69	35	-2548.0537	5166.1074	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2404.1885	5073.3395	0.6410	0.6410
HKYI	40	-2404.8520	5074.6666	0.3301	0.9711
HKYIG	41	-2404.2239	5080.0345	0.0225	0.9936
GTRG	44	-2395.9120	5083.2830	0.0044	0.9980
GTRI	44	-2396.8199	5085.0987	0.0018	0.9998
GTRIG	45	-2395.9119	5089.9067	0.0002	1.0000
K2PG	37	-2441.1545	5127.3993	0.0000	1.0000
K2PI	37	-2441.2861	5127.6626	0.0000	1.0000
K2PIG	38	-2441.1679	5134.0502	0.0000	1.0000
HKY	39	-2442.2631	5142.8648	0.0000	1.0000
GTR	43	-2431.4486	5147.7320	0.0000	1.0000
SYMG	41	-2440.2351	5152.0568	0.0000	1.0000
SYMI	41	-2440.4106	5152.4078	0.0000	1.0000
SYMIG	42	-2440.2348	5158.6804	0.0000	1.0000
K2P	36	-2482.6837	5203.8338	0.0000	1.0000
F81G	39	-2477.5197	5213.3779	0.0000	1.0000
F81I	39	-2477.5584	5213.4553	0.0000	1.0000
F81IG	40	-2477.6629	5220.2884	0.0000	1.0000
SYM	40	-2480.3163	5225.5952	0.0000	1.0000
JC69G	36	-2508.5192	5255.5048	0.0000	1.0000
JC69I	36	-2508.5244	5255.5151	0.0000	1.0000
JC69IG	37	-2508.5191	5262.1285	0.0000	1.0000
F81	38	-2515.0972	5281.9089	0.0000	1.0000
JC69	35	-2548.0537	5327.9497	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/chr7_10860.phylip = 1 - 753;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10860.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/chr7_10860.phylip = 1 - 753;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10860.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/chr7_10860.phylip = 1 - 753;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10860.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

