
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:03 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_2784.phylip" (19 taxa, 299 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1072.0670	2247.7245	0.5139	0.5139
GTRG	44	-1072.5646	2248.7198	0.3124	0.8263
GTRIG	45	-1072.0760	2250.5157	0.1273	0.9535
HKYG	40	-1080.6390	2253.9912	0.0224	0.9759
HKYI	40	-1080.8470	2254.4072	0.0182	0.9941
HKYIG	41	-1080.6401	2256.6809	0.0058	0.9999
GTR	43	-1082.5423	2265.9239	0.0001	1.0000
HKY	39	-1090.0294	2270.1052	0.0000	1.0000
K2PI	37	-1095.9436	2276.6612	0.0000	1.0000
K2PG	37	-1095.9847	2276.7433	0.0000	1.0000
SYMI	41	-1091.0239	2277.4486	0.0000	1.0000
SYMG	41	-1091.5293	2278.4594	0.0000	1.0000
K2PIG	38	-1095.9174	2279.2348	0.0000	1.0000
SYMIG	42	-1091.0309	2280.1713	0.0000	1.0000
F81I	39	-1096.4788	2283.0040	0.0000	1.0000
F81G	39	-1096.7793	2283.6050	0.0000	1.0000
F81IG	40	-1096.4808	2285.6748	0.0000	1.0000
K2P	36	-1105.8765	2293.9210	0.0000	1.0000
SYM	40	-1101.2876	2295.2885	0.0000	1.0000
F81	38	-1105.6206	2298.6412	0.0000	1.0000
JC69I	36	-1108.9221	2300.0122	0.0000	1.0000
JC69G	36	-1109.3559	2300.8797	0.0000	1.0000
JC69IG	37	-1108.9274	2302.6287	0.0000	1.0000
JC69	35	-1118.5262	2316.6342	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1072.0670	2232.1339	0.5012	0.5012
GTRG	44	-1072.5646	2233.1292	0.3047	0.8059
GTRIG	45	-1072.0760	2234.1520	0.1827	0.9887
HKYG	40	-1080.6390	2241.2781	0.0052	0.9938
HKYI	40	-1080.8470	2241.6940	0.0042	0.9981
HKYIG	41	-1080.6401	2243.2802	0.0019	1.0000
GTR	43	-1082.5423	2251.0847	0.0000	1.0000
HKY	39	-1090.0294	2258.0588	0.0000	1.0000
SYMI	41	-1091.0239	2264.0478	0.0000	1.0000
SYMG	41	-1091.5293	2265.0586	0.0000	1.0000
K2PI	37	-1095.9436	2265.8872	0.0000	1.0000
K2PG	37	-1095.9847	2265.9693	0.0000	1.0000
SYMIG	42	-1091.0309	2266.0619	0.0000	1.0000
K2PIG	38	-1095.9174	2267.8348	0.0000	1.0000
F81I	39	-1096.4788	2270.9576	0.0000	1.0000
F81G	39	-1096.7793	2271.5586	0.0000	1.0000
F81IG	40	-1096.4808	2272.9616	0.0000	1.0000
SYM	40	-1101.2876	2282.5753	0.0000	1.0000
K2P	36	-1105.8765	2283.7530	0.0000	1.0000
F81	38	-1105.6206	2287.2412	0.0000	1.0000
JC69I	36	-1108.9221	2289.8443	0.0000	1.0000
JC69G	36	-1109.3559	2290.7118	0.0000	1.0000
JC69IG	37	-1108.9274	2291.8548	0.0000	1.0000
JC69	35	-1118.5262	2307.0525	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1080.6390	2389.2958	0.5070	0.5070
HKYI	40	-1080.8470	2389.7117	0.4118	0.9189
GTRI	44	-1072.0670	2394.9535	0.0300	0.9488
HKYIG	41	-1080.6401	2394.9983	0.0293	0.9781
GTRG	44	-1072.5646	2395.9488	0.0182	0.9963
GTRIG	45	-1072.0760	2400.6720	0.0017	0.9981
HKY	39	-1090.0294	2402.3761	0.0007	0.9988
K2PI	37	-1095.9436	2402.8036	0.0006	0.9994
K2PG	37	-1095.9847	2402.8857	0.0006	0.9999
K2PIG	38	-1095.9174	2408.4516	0.0000	1.0000
GTR	43	-1082.5423	2410.2037	0.0000	1.0000
F81I	39	-1096.4788	2415.2749	0.0000	1.0000
SYMI	41	-1091.0239	2415.7660	0.0000	1.0000
F81G	39	-1096.7793	2415.8759	0.0000	1.0000
SYMG	41	-1091.5293	2416.7768	0.0000	1.0000
K2P	36	-1105.8765	2416.9690	0.0000	1.0000
F81IG	40	-1096.4808	2420.9793	0.0000	1.0000
SYMIG	42	-1091.0309	2421.4805	0.0000	1.0000
JC69I	36	-1108.9221	2423.0602	0.0000	1.0000
JC69G	36	-1109.3559	2423.9278	0.0000	1.0000
F81	38	-1105.6206	2427.8581	0.0000	1.0000
JC69IG	37	-1108.9274	2428.7712	0.0000	1.0000
SYM	40	-1101.2876	2430.5930	0.0000	1.0000
JC69	35	-1118.5262	2436.5680	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2784.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2784.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2784.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2784.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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_2784.phylip = 1 - 299;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2784.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;


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

