
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:09 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/chr8_6230.phylip" (19 taxa, 240 characters)

Minimum AIC  model: HKYI
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	-458.6173	1010.8346	0.2157	0.2157
K2P	36	-463.1307	1011.3845	0.1638	0.3795
HKYI	40	-457.5811	1011.6447	0.1438	0.5233
HKYG	40	-457.5932	1011.6688	0.1421	0.6655
K2PI	37	-462.0277	1011.9762	0.1219	0.7873
K2PG	37	-462.0380	1011.9969	0.1206	0.9079
HKYIG	41	-457.6035	1014.6010	0.0328	0.9407
K2PIG	38	-462.0490	1014.8443	0.0290	0.9698
GTR	43	-456.0925	1017.4911	0.0077	0.9775
SYM	40	-460.9489	1018.3803	0.0050	0.9825
GTRI	44	-455.1360	1018.5797	0.0045	0.9870
GTRG	44	-455.1531	1018.6138	0.0044	0.9914
SYMI	41	-460.0032	1019.4004	0.0030	0.9944
SYMG	41	-460.0227	1019.4393	0.0029	0.9973
GTRIG	45	-455.1629	1021.6660	0.0010	0.9982
SYMIG	42	-460.0318	1022.3986	0.0007	0.9989
F81	38	-466.7341	1024.2144	0.0003	0.9992
JC69	35	-471.2416	1024.8361	0.0002	0.9994
F81I	39	-465.8038	1025.2077	0.0002	0.9995
F81G	39	-465.8191	1025.2381	0.0002	0.9997
JC69I	36	-470.3166	1025.7564	0.0001	0.9998
JC69G	36	-470.3332	1025.7896	0.0001	0.9999
F81IG	40	-465.8272	1028.1368	0.0000	1.0000
JC69IG	37	-470.3338	1028.5884	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-457.5811	995.1623	0.2038	0.2038
HKYG	40	-457.5932	995.1864	0.2014	0.4052
HKY	39	-458.6173	995.2346	0.1966	0.6017
HKYIG	41	-457.6035	997.2070	0.0733	0.6751
K2PI	37	-462.0277	998.0554	0.0480	0.7230
K2PG	37	-462.0380	998.0761	0.0475	0.7705
GTR	43	-456.0925	998.1850	0.0450	0.8155
K2P	36	-463.1307	998.2613	0.0433	0.8587
GTRI	44	-455.1360	998.2720	0.0430	0.9018
GTRG	44	-455.1531	998.3061	0.0423	0.9441
K2PIG	38	-462.0490	1000.0980	0.0173	0.9614
GTRIG	45	-455.1629	1000.3258	0.0154	0.9768
SYM	40	-460.9489	1001.8979	0.0070	0.9838
SYMI	41	-460.0032	1002.0064	0.0067	0.9905
SYMG	41	-460.0227	1002.0454	0.0065	0.9970
SYMIG	42	-460.0318	1004.0636	0.0024	0.9994
F81	38	-466.7341	1009.4681	0.0002	0.9995
F81I	39	-465.8038	1009.6077	0.0001	0.9997
F81G	39	-465.8191	1009.6381	0.0001	0.9998
F81IG	40	-465.8272	1011.6544	0.0001	0.9999
JC69	35	-471.2416	1012.4831	0.0000	0.9999
JC69I	36	-470.3166	1012.6332	0.0000	1.0000
JC69G	36	-470.3332	1012.6664	0.0000	1.0000
JC69IG	37	-470.3338	1014.6676	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-463.1307	1123.5643	0.6947	0.6947
K2PI	37	-462.0277	1126.8391	0.1351	0.8298
K2PG	37	-462.0380	1126.8597	0.1337	0.9635
HKY	39	-458.6173	1130.9795	0.0170	0.9805
K2PIG	38	-462.0490	1132.3623	0.0085	0.9891
JC69	35	-471.2416	1134.3055	0.0032	0.9923
HKYI	40	-457.5811	1134.3878	0.0031	0.9954
HKYG	40	-457.5932	1134.4120	0.0031	0.9985
JC69I	36	-470.3166	1137.9362	0.0005	0.9990
JC69G	36	-470.3332	1137.9694	0.0005	0.9995
HKYIG	41	-457.6035	1139.9132	0.0002	0.9997
SYM	40	-460.9489	1141.1234	0.0001	0.9998
F81	38	-466.7341	1141.7324	0.0001	0.9999
JC69IG	37	-470.3338	1143.4512	0.0000	0.9999
SYMI	41	-460.0032	1144.7126	0.0000	1.0000
SYMG	41	-460.0227	1144.7516	0.0000	1.0000
F81I	39	-465.8038	1145.3526	0.0000	1.0000
F81G	39	-465.8191	1145.3830	0.0000	1.0000
GTR	43	-456.0925	1147.8524	0.0000	1.0000
SYMIG	42	-460.0318	1150.2504	0.0000	1.0000
F81IG	40	-465.8272	1150.8800	0.0000	1.0000
GTRI	44	-455.1360	1151.4201	0.0000	1.0000
GTRG	44	-455.1531	1151.4542	0.0000	1.0000
GTRIG	45	-455.1629	1156.9546	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6230.phylip = 1 - 240;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6230.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
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/chr8_6230.phylip = 1 - 240;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6230.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/chr8_6230.phylip = 1 - 240;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_6230.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

