
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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/chr4_7606.phylip" (19 taxa, 138 characters)

Minimum AIC  model: HKYG
Minimum AICc model: K2P
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
K2P	36	-476.2154	1050.8070	0.2546	0.2546
HKY	39	-470.7077	1051.2522	0.2038	0.4583
K2PI	37	-474.7129	1051.5457	0.1759	0.6342
K2PG	37	-474.7153	1051.5505	0.1755	0.8098
HKYG	40	-469.6776	1053.1696	0.0781	0.8879
HKYI	40	-469.7702	1053.3549	0.0712	0.9591
K2PIG	38	-474.7151	1055.3696	0.0260	0.9851
HKYIG	41	-469.6950	1057.2650	0.0101	0.9952
SYM	40	-473.7095	1061.2335	0.0014	0.9966
SYMI	41	-471.7278	1061.3305	0.0013	0.9979
SYMG	41	-471.9375	1061.7500	0.0011	0.9989
GTR	43	-468.6039	1063.4632	0.0005	0.9994
GTRI	44	-467.2349	1065.0505	0.0002	0.9996
GTRG	44	-467.3973	1065.3752	0.0002	0.9998
SYMIG	42	-471.7332	1065.4875	0.0002	0.9999
GTRIG	45	-467.2381	1069.4763	0.0000	1.0000
JC69	35	-488.1816	1071.0690	0.0000	1.0000
JC69I	36	-486.7362	1071.8487	0.0000	1.0000
JC69G	36	-486.7574	1071.8910	0.0000	1.0000
F81	38	-483.6426	1073.2247	0.0000	1.0000
F81G	39	-482.4629	1074.7626	0.0000	1.0000
F81I	39	-482.4721	1074.7809	0.0000	1.0000
JC69IG	37	-486.7537	1075.6274	0.0000	1.0000
F81IG	40	-482.4611	1078.7366	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-469.6776	1019.3552	0.2291	0.2291
HKY	39	-470.7077	1019.4155	0.2223	0.4514
HKYI	40	-469.7702	1019.5405	0.2088	0.6602
HKYIG	41	-469.6950	1021.3900	0.0828	0.7430
GTRI	44	-467.2349	1022.4699	0.0483	0.7913
GTRG	44	-467.3973	1022.7945	0.0410	0.8324
GTR	43	-468.6039	1023.2079	0.0334	0.8657
K2PI	37	-474.7129	1023.4257	0.0299	0.8957
K2PG	37	-474.7153	1023.4305	0.0299	0.9255
K2P	36	-476.2154	1024.4308	0.0181	0.9436
GTRIG	45	-467.2381	1024.4763	0.0177	0.9613
K2PIG	38	-474.7151	1025.4302	0.0110	0.9723
SYMI	41	-471.7278	1025.4555	0.0108	0.9832
SYMG	41	-471.9375	1025.8750	0.0088	0.9920
SYM	40	-473.7095	1027.4190	0.0041	0.9960
SYMIG	42	-471.7332	1027.4664	0.0040	1.0000
F81G	39	-482.4629	1042.9258	0.0000	1.0000
F81I	39	-482.4721	1042.9442	0.0000	1.0000
F81	38	-483.6426	1043.2853	0.0000	1.0000
F81IG	40	-482.4611	1044.9222	0.0000	1.0000
JC69I	36	-486.7362	1045.4724	0.0000	1.0000
JC69G	36	-486.7574	1045.5147	0.0000	1.0000
JC69	35	-488.1816	1046.3631	0.0000	1.0000
JC69IG	37	-486.7537	1047.5074	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-476.2154	1129.8119	0.4944	0.4944
K2PI	37	-474.7129	1131.7341	0.1891	0.6835
K2PG	37	-474.7153	1131.7389	0.1886	0.8721
HKY	39	-470.7077	1133.5784	0.0752	0.9473
HKYG	40	-469.6776	1136.4453	0.0179	0.9653
HKYI	40	-469.7702	1136.6306	0.0163	0.9816
K2PIG	38	-474.7151	1136.6658	0.0161	0.9977
HKYIG	41	-469.6950	1141.4074	0.0015	0.9992
SYM	40	-473.7095	1144.5092	0.0003	0.9995
SYMI	41	-471.7278	1145.4729	0.0002	0.9997
SYMG	41	-471.9375	1145.8924	0.0002	0.9999
JC69	35	-488.1816	1148.8170	0.0000	0.9999
GTR	43	-468.6039	1149.0798	0.0000	0.9999
SYMIG	42	-471.7332	1150.4111	0.0000	0.9999
JC69I	36	-486.7362	1150.8536	0.0000	1.0000
JC69G	36	-486.7574	1150.8959	0.0000	1.0000
GTRI	44	-467.2349	1151.2690	0.0000	1.0000
GTRG	44	-467.3973	1151.5937	0.0000	1.0000
F81	38	-483.6426	1154.5209	0.0000	1.0000
JC69IG	37	-486.7537	1155.8158	0.0000	1.0000
GTRIG	45	-467.2381	1156.2027	0.0000	1.0000
F81G	39	-482.4629	1157.0887	0.0000	1.0000
F81I	39	-482.4721	1157.1071	0.0000	1.0000
F81IG	40	-482.4611	1162.0123	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7606.phylip = 1 - 138;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7606.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7606.phylip = 1 - 138;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7606.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) 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/chr4_7606.phylip = 1 - 138;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7606.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


-------------------------------------------------------------
End of Output

