
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:44 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/chr6_4125.phylip" (19 taxa, 203 characters)

Minimum AIC  model: HKY
Minimum AICc model: HKY
Minimum BIC  model: K2P


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
HKY	39	-403.7309	904.6030	0.5306	0.5306
K2P	36	-409.7122	907.4727	0.1264	0.6570
HKYG	40	-403.7261	907.6991	0.1128	0.7698
HKYI	40	-403.7277	907.7022	0.1127	0.8825
K2PI	37	-409.6907	910.4238	0.0289	0.9114
K2PG	37	-409.6925	910.4274	0.0288	0.9402
HKYIG	41	-403.7259	910.8431	0.0234	0.9637
GTR	43	-400.8557	911.5101	0.0168	0.9804
K2PIG	38	-409.6907	913.4545	0.0063	0.9868
GTRG	44	-400.8564	914.7762	0.0033	0.9901
GTRI	44	-400.8587	914.7808	0.0033	0.9933
SYM	40	-407.5079	915.2628	0.0026	0.9959
F81	38	-411.4321	916.9373	0.0011	0.9970
GTRIG	45	-400.8591	918.0877	0.0006	0.9977
SYMG	41	-407.5047	918.4007	0.0005	0.9982
SYMI	41	-407.5065	918.4043	0.0005	0.9987
JC69	35	-416.8995	918.8888	0.0004	0.9991
F81G	39	-411.4299	920.0009	0.0002	0.9994
F81I	39	-411.4315	920.0041	0.0002	0.9996
SYMIG	42	-407.5051	921.5852	0.0001	0.9997
JC69G	36	-416.8935	921.8351	0.0001	0.9998
JC69I	36	-416.8938	921.8357	0.0001	0.9999
F81IG	40	-411.4303	923.1076	0.0001	1.0000
JC69IG	37	-416.8921	924.8266	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKY	39	-403.7309	885.4619	0.3852	0.3852
HKYG	40	-403.7261	887.4522	0.1424	0.5276
HKYI	40	-403.7277	887.4553	0.1422	0.6698
GTR	43	-400.8557	887.7114	0.1251	0.7949
HKYIG	41	-403.7259	889.4518	0.0524	0.8473
GTRG	44	-400.8564	889.7129	0.0460	0.8933
GTRI	44	-400.8587	889.7175	0.0459	0.9392
K2P	36	-409.7122	891.4245	0.0195	0.9587
GTRIG	45	-400.8591	891.7183	0.0169	0.9756
K2PI	37	-409.6907	893.3814	0.0073	0.9829
K2PG	37	-409.6925	893.3850	0.0073	0.9903
SYM	40	-407.5079	895.0159	0.0032	0.9935
K2PIG	38	-409.6907	895.3813	0.0027	0.9962
SYMG	41	-407.5047	897.0094	0.0012	0.9974
SYMI	41	-407.5065	897.0130	0.0012	0.9986
F81	38	-411.4321	898.8641	0.0005	0.9991
SYMIG	42	-407.5051	899.0102	0.0004	0.9995
F81G	39	-411.4299	900.8598	0.0002	0.9997
F81I	39	-411.4315	900.8630	0.0002	0.9999
F81IG	40	-411.4303	902.8607	0.0001	0.9999
JC69	35	-416.8995	903.7990	0.0000	1.0000
JC69G	36	-416.8935	905.7869	0.0000	1.0000
JC69I	36	-416.8938	905.7875	0.0000	1.0000
JC69IG	37	-416.8921	907.7842	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-409.7122	1010.6999	0.7582	0.7582
HKY	39	-403.7309	1014.6769	0.1038	0.8620
K2PI	37	-409.6907	1015.9700	0.0544	0.9164
K2PG	37	-409.6925	1015.9736	0.0543	0.9707
JC69	35	-416.8995	1019.7612	0.0082	0.9788
HKYG	40	-403.7261	1019.9805	0.0073	0.9862
HKYI	40	-403.7277	1019.9836	0.0073	0.9935
K2PIG	38	-409.6907	1021.2832	0.0038	0.9973
F81	38	-411.4321	1024.7659	0.0007	0.9980
JC69G	36	-416.8935	1025.0624	0.0006	0.9985
JC69I	36	-416.8938	1025.0630	0.0006	0.9991
HKYIG	41	-403.7259	1025.2933	0.0005	0.9996
SYM	40	-407.5079	1027.5441	0.0002	0.9998
F81G	39	-411.4299	1030.0748	0.0000	0.9998
F81I	39	-411.4315	1030.0780	0.0000	0.9999
GTR	43	-400.8557	1030.1793	0.0000	0.9999
JC69IG	37	-416.8921	1030.3728	0.0000	1.0000
SYMG	41	-407.5047	1032.8508	0.0000	1.0000
SYMI	41	-407.5065	1032.8544	0.0000	1.0000
F81IG	40	-411.4303	1035.3889	0.0000	1.0000
GTRG	44	-400.8564	1035.4939	0.0000	1.0000
GTRI	44	-400.8587	1035.4985	0.0000	1.0000
SYMIG	42	-407.5051	1038.1649	0.0000	1.0000
GTRIG	45	-400.8591	1040.8126	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


[Mrbayes block for the best BIC model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4125.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

