
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:35 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_2305.phylip" (19 taxa, 611 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
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
SYMG	41	-2400.7187	4889.4902	0.3636	0.3636
K2PG	37	-2405.9871	4890.8817	0.1814	0.5450
SYMI	41	-2401.6635	4891.3796	0.1414	0.6864
SYMIG	42	-2400.5807	4891.5206	0.1318	0.8181
K2PIG	38	-2405.8721	4892.9261	0.0652	0.8834
GTRG	44	-2399.3855	4893.7674	0.0428	0.9262
K2PI	37	-2408.0196	4894.9466	0.0238	0.9500
GTRIG	45	-2399.2564	4895.8401	0.0152	0.9652
GTRI	44	-2400.4428	4895.8821	0.0149	0.9801
HKYG	40	-2405.1463	4896.0470	0.0137	0.9938
HKYIG	41	-2405.0486	4898.1500	0.0048	0.9986
HKYI	40	-2407.3957	4900.5459	0.0014	1.0000
SYM	40	-2431.2976	4948.3496	0.0000	1.0000
GTR	43	-2429.7513	4952.1764	0.0000	1.0000
K2P	36	-2437.9532	4952.5475	0.0000	1.0000
HKY	39	-2436.9570	4957.3780	0.0000	1.0000
JC69G	36	-2469.6802	5016.0014	0.0000	1.0000
JC69I	36	-2471.3450	5019.3311	0.0000	1.0000
F81G	39	-2468.5452	5020.5545	0.0000	1.0000
JC69IG	37	-2471.1996	5021.3066	0.0000	1.0000
F81I	39	-2470.3326	5024.1294	0.0000	1.0000
F81IG	40	-2470.0093	5025.7730	0.0000	1.0000
JC69	35	-2499.5994	5073.5814	0.0000	1.0000
F81	38	-2498.5019	5078.1856	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-2400.7187	4883.4375	0.3805	0.3805
SYMIG	42	-2400.5807	4885.1614	0.1607	0.5412
SYMI	41	-2401.6635	4885.3269	0.1479	0.6892
K2PG	37	-2405.9871	4885.9742	0.1070	0.7962
GTRG	44	-2399.3855	4886.7710	0.0719	0.8681
K2PIG	38	-2405.8721	4887.7443	0.0442	0.9123
GTRIG	45	-2399.2564	4888.5127	0.0301	0.9423
GTRI	44	-2400.4428	4888.8856	0.0250	0.9673
K2PI	37	-2408.0196	4890.0391	0.0140	0.9813
HKYG	40	-2405.1463	4890.2926	0.0124	0.9937
HKYIG	41	-2405.0486	4892.0972	0.0050	0.9987
HKYI	40	-2407.3957	4894.7915	0.0013	1.0000
SYM	40	-2431.2976	4942.5953	0.0000	1.0000
GTR	43	-2429.7513	4945.5026	0.0000	1.0000
K2P	36	-2437.9532	4947.9064	0.0000	1.0000
HKY	39	-2436.9570	4951.9139	0.0000	1.0000
JC69G	36	-2469.6802	5011.3603	0.0000	1.0000
JC69I	36	-2471.3450	5014.6899	0.0000	1.0000
F81G	39	-2468.5452	5015.0904	0.0000	1.0000
JC69IG	37	-2471.1996	5016.3991	0.0000	1.0000
F81I	39	-2470.3326	5018.6653	0.0000	1.0000
F81IG	40	-2470.0093	5020.0187	0.0000	1.0000
JC69	35	-2499.5994	5069.1988	0.0000	1.0000
F81	38	-2498.5019	5073.0038	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2405.9871	5049.3327	0.8494	0.8494
K2PI	37	-2408.0196	5053.3977	0.1113	0.9607
K2PIG	38	-2405.8721	5055.5180	0.0385	0.9992
SYMG	41	-2400.7187	5064.4565	0.0004	0.9997
SYMI	41	-2401.6635	5066.3459	0.0002	0.9998
HKYG	40	-2405.1463	5066.8965	0.0001	1.0000
SYMIG	42	-2400.5807	5070.5955	0.0000	1.0000
HKYI	40	-2407.3957	5071.3954	0.0000	1.0000
HKYIG	41	-2405.0486	5073.1162	0.0000	1.0000
GTRG	44	-2399.3855	5081.0352	0.0000	1.0000
GTRI	44	-2400.4428	5083.1499	0.0000	1.0000
GTRIG	45	-2399.2564	5087.1921	0.0000	1.0000
K2P	36	-2437.9532	5106.8499	0.0000	1.0000
SYM	40	-2431.2976	5119.1991	0.0000	1.0000
HKY	39	-2436.9570	5124.1027	0.0000	1.0000
GTR	43	-2429.7513	5135.3518	0.0000	1.0000
JC69G	36	-2469.6802	5170.3038	0.0000	1.0000
JC69I	36	-2471.3450	5173.6334	0.0000	1.0000
JC69IG	37	-2471.1996	5179.7577	0.0000	1.0000
F81G	39	-2468.5452	5187.2792	0.0000	1.0000
F81I	39	-2470.3326	5190.8541	0.0000	1.0000
F81IG	40	-2470.0093	5196.6225	0.0000	1.0000
JC69	35	-2499.5994	5223.7272	0.0000	1.0000
F81	38	-2498.5019	5240.7775	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2305.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2305.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_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=Fixed(Equal);
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/chr5_2305.phylip = 1 - 611;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2305.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

