
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:25 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/chrZ_7923.phylip" (19 taxa, 712 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2911.4819	5916.9008	0.6728	0.6728
GTRIG	45	-2911.0775	5918.3712	0.3226	0.9954
HKYG	40	-2921.4054	5927.6990	0.0030	0.9985
HKYIG	41	-2920.9688	5929.0778	0.0015	1.0000
GTRI	44	-2921.7824	5937.5019	0.0000	1.0000
HKYI	40	-2930.9774	5946.8430	0.0000	1.0000
SYMG	41	-2935.0412	5957.2227	0.0000	1.0000
SYMIG	42	-2934.5241	5958.4473	0.0000	1.0000
K2PG	37	-2944.5174	5967.2069	0.0000	1.0000
K2PIG	38	-2944.0365	5968.4772	0.0000	1.0000
SYMI	41	-2944.4541	5976.0485	0.0000	1.0000
K2PI	37	-2953.7027	5985.5775	0.0000	1.0000
GTR	43	-2974.2466	6040.1578	0.0000	1.0000
HKY	39	-2985.5125	6053.6679	0.0000	1.0000
SYM	40	-3001.6985	6088.2852	0.0000	1.0000
K2P	36	-3011.4027	6098.7520	0.0000	1.0000
F81G	39	-3018.7852	6120.2132	0.0000	1.0000
F81IG	40	-3018.3087	6121.5056	0.0000	1.0000
JC69G	36	-3036.6701	6149.2868	0.0000	1.0000
F81I	39	-3033.5643	6149.7715	0.0000	1.0000
JC69IG	37	-3036.1435	6150.4590	0.0000	1.0000
JC69I	36	-3045.1793	6166.3053	0.0000	1.0000
F81	38	-3088.5887	6257.5815	0.0000	1.0000
JC69	35	-3108.6559	6291.0396	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2911.4819	5910.9638	0.6429	0.6429
GTRIG	45	-2911.0775	5912.1550	0.3544	0.9973
HKYG	40	-2921.4054	5922.8108	0.0017	0.9990
HKYIG	41	-2920.9688	5923.9375	0.0010	1.0000
GTRI	44	-2921.7824	5931.5649	0.0000	1.0000
HKYI	40	-2930.9774	5941.9548	0.0000	1.0000
SYMG	41	-2935.0412	5952.0824	0.0000	1.0000
SYMIG	42	-2934.5241	5953.0482	0.0000	1.0000
K2PG	37	-2944.5174	5963.0348	0.0000	1.0000
K2PIG	38	-2944.0365	5964.0730	0.0000	1.0000
SYMI	41	-2944.4541	5970.9082	0.0000	1.0000
K2PI	37	-2953.7027	5981.4054	0.0000	1.0000
GTR	43	-2974.2466	6034.4931	0.0000	1.0000
HKY	39	-2985.5125	6049.0251	0.0000	1.0000
SYM	40	-3001.6985	6083.3970	0.0000	1.0000
K2P	36	-3011.4027	6094.8054	0.0000	1.0000
F81G	39	-3018.7852	6115.5703	0.0000	1.0000
F81IG	40	-3018.3087	6116.6174	0.0000	1.0000
F81I	39	-3033.5643	6145.1287	0.0000	1.0000
JC69G	36	-3036.6701	6145.3401	0.0000	1.0000
JC69IG	37	-3036.1435	6146.2869	0.0000	1.0000
JC69I	36	-3045.1793	6162.3586	0.0000	1.0000
F81	38	-3088.5887	6253.1773	0.0000	1.0000
JC69	35	-3108.6559	6287.3117	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2921.4054	6105.5339	0.9086	0.9086
HKYIG	41	-2920.9688	6111.2287	0.0527	0.9613
GTRG	44	-2911.4819	6111.9592	0.0366	0.9979
GTRIG	45	-2911.0775	6117.7185	0.0021	0.9999
HKYI	40	-2930.9774	6124.6779	0.0001	1.0000
K2PG	37	-2944.5174	6132.0537	0.0000	1.0000
GTRI	44	-2921.7824	6132.5603	0.0000	1.0000
K2PIG	38	-2944.0365	6137.6600	0.0000	1.0000
SYMG	41	-2935.0412	6139.3736	0.0000	1.0000
SYMIG	42	-2934.5241	6144.9075	0.0000	1.0000
K2PI	37	-2953.7027	6150.4242	0.0000	1.0000
SYMI	41	-2944.4541	6158.1994	0.0000	1.0000
HKY	39	-2985.5125	6227.1801	0.0000	1.0000
GTR	43	-2974.2466	6230.9205	0.0000	1.0000
K2P	36	-3011.4027	6259.2562	0.0000	1.0000
SYM	40	-3001.6985	6266.1201	0.0000	1.0000
F81G	39	-3018.7852	6293.7253	0.0000	1.0000
F81IG	40	-3018.3087	6299.3405	0.0000	1.0000
JC69G	36	-3036.6701	6309.7909	0.0000	1.0000
JC69IG	37	-3036.1435	6315.3058	0.0000	1.0000
F81I	39	-3033.5643	6323.2837	0.0000	1.0000
JC69I	36	-3045.1793	6326.8094	0.0000	1.0000
F81	38	-3088.5887	6426.7643	0.0000	1.0000
JC69	35	-3108.6559	6447.1945	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7923.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7923.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7923.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7923.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) 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/chrZ_7923.phylip = 1 - 712;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7923.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;


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End of Output

