
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:13 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/chr1_5427.phylip" (19 taxa, 890 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-2886.6840	5857.2314	0.4063	0.4063
HKYIG	41	-2886.2441	5858.5495	0.2102	0.6165
GTRG	44	-2883.3349	5859.3562	0.1404	0.7569
HKYI	40	-2887.8581	5859.5795	0.1256	0.8825
GTRIG	45	-2882.7520	5860.4092	0.0829	0.9655
GTRI	44	-2884.7377	5862.1618	0.0345	1.0000
K2PG	37	-2921.9556	5921.2116	0.0000	1.0000
K2PIG	38	-2921.6040	5922.6910	0.0000	1.0000
K2PI	37	-2923.0509	5923.4022	0.0000	1.0000
SYMG	41	-2921.5231	5929.1076	0.0000	1.0000
SYMIG	42	-2921.1682	5930.6008	0.0000	1.0000
SYMI	41	-2922.6302	5931.3217	0.0000	1.0000
F81G	39	-2930.6019	5942.8743	0.0000	1.0000
F81IG	40	-2930.2907	5944.4448	0.0000	1.0000
F81I	39	-2931.4840	5944.6387	0.0000	1.0000
JC69G	36	-2959.9729	5995.0688	0.0000	1.0000
HKY	39	-2957.4468	5996.5641	0.0000	1.0000
JC69I	36	-2960.8567	5996.8365	0.0000	1.0000
JC69IG	37	-2959.8885	5997.0774	0.0000	1.0000
GTR	43	-2954.9897	6000.4521	0.0000	1.0000
K2P	36	-2991.2882	6057.6996	0.0000	1.0000
SYM	40	-2990.6690	6065.2013	0.0000	1.0000
F81	38	-2998.7568	6076.9966	0.0000	1.0000
JC69	35	-3028.1184	6129.1876	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2886.6840	5853.3681	0.3480	0.3480
HKYIG	41	-2886.2441	5854.4882	0.1987	0.5467
GTRG	44	-2883.3349	5854.6698	0.1815	0.7282
GTRIG	45	-2882.7520	5855.5040	0.1196	0.8478
HKYI	40	-2887.8581	5855.7162	0.1076	0.9554
GTRI	44	-2884.7377	5857.4754	0.0446	1.0000
K2PG	37	-2921.9556	5917.9111	0.0000	1.0000
K2PIG	38	-2921.6040	5919.2081	0.0000	1.0000
K2PI	37	-2923.0509	5920.1017	0.0000	1.0000
SYMG	41	-2921.5231	5925.0462	0.0000	1.0000
SYMIG	42	-2921.1682	5926.3363	0.0000	1.0000
SYMI	41	-2922.6302	5927.2603	0.0000	1.0000
F81G	39	-2930.6019	5939.2037	0.0000	1.0000
F81IG	40	-2930.2907	5940.5814	0.0000	1.0000
F81I	39	-2931.4840	5940.9681	0.0000	1.0000
JC69G	36	-2959.9729	5991.9457	0.0000	1.0000
HKY	39	-2957.4468	5992.8935	0.0000	1.0000
JC69I	36	-2960.8567	5993.7134	0.0000	1.0000
JC69IG	37	-2959.8885	5993.7770	0.0000	1.0000
GTR	43	-2954.9897	5995.9793	0.0000	1.0000
K2P	36	-2991.2882	6054.5765	0.0000	1.0000
SYM	40	-2990.6690	6061.3380	0.0000	1.0000
F81	38	-2998.7568	6073.5137	0.0000	1.0000
JC69	35	-3028.1184	6126.2368	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2886.6840	6045.0169	0.7346	0.7346
HKYI	40	-2887.8581	6047.3650	0.2271	0.9617
HKYIG	41	-2886.2441	6050.9283	0.0382	1.0000
GTRG	44	-2883.3349	6065.4836	0.0000	1.0000
GTRI	44	-2884.7377	6068.2891	0.0000	1.0000
GTRIG	45	-2882.7520	6071.1090	0.0000	1.0000
K2PG	37	-2921.9556	6095.1863	0.0000	1.0000
K2PI	37	-2923.0509	6097.3769	0.0000	1.0000
K2PIG	38	-2921.6040	6101.2745	0.0000	1.0000
SYMG	41	-2921.5231	6121.4863	0.0000	1.0000
SYMI	41	-2922.6302	6123.7004	0.0000	1.0000
F81G	39	-2930.6019	6126.0614	0.0000	1.0000
SYMIG	42	-2921.1682	6127.5676	0.0000	1.0000
F81I	39	-2931.4840	6127.8257	0.0000	1.0000
F81IG	40	-2930.2907	6132.2303	0.0000	1.0000
JC69G	36	-2959.9729	6164.4297	0.0000	1.0000
JC69I	36	-2960.8567	6166.1974	0.0000	1.0000
JC69IG	37	-2959.8885	6171.0522	0.0000	1.0000
HKY	39	-2957.4468	6179.7512	0.0000	1.0000
GTR	43	-2954.9897	6202.0018	0.0000	1.0000
K2P	36	-2991.2882	6227.0605	0.0000	1.0000
SYM	40	-2990.6690	6252.9868	0.0000	1.0000
F81	38	-2998.7568	6255.5801	0.0000	1.0000
JC69	35	-3028.1184	6293.9295	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/chr1_5427.phylip = 1 - 890;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5427.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5427.phylip = 1 - 890;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5427.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5427.phylip = 1 - 890;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5427.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

