
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:36 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_7199.phylip" (19 taxa, 780 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	-2867.4445	5819.3275	0.5201	0.5201
HKYIG	41	-2866.4546	5819.5759	0.4594	0.9795
GTRG	44	-2866.4078	5826.2034	0.0167	0.9962
GTRIG	45	-2866.8901	5829.4205	0.0033	0.9996
HKYI	40	-2874.5491	5833.5367	0.0004	1.0000
GTRI	44	-2874.2111	5841.8100	0.0000	1.0000
K2PG	37	-2885.0252	5847.8401	0.0000	1.0000
K2PIG	38	-2884.1066	5848.2132	0.0000	1.0000
SYMG	41	-2884.8895	5856.4457	0.0000	1.0000
K2PI	37	-2891.8653	5861.5204	0.0000	1.0000
SYMIG	42	-2887.2591	5863.4191	0.0000	1.0000
SYMI	41	-2894.1097	5874.8861	0.0000	1.0000
HKY	39	-2927.7300	5937.6763	0.0000	1.0000
GTR	43	-2926.6550	5944.4513	0.0000	1.0000
K2P	36	-2946.5926	5968.7707	0.0000	1.0000
SYM	40	-2946.4818	5977.4021	0.0000	1.0000
F81G	39	-2955.7066	5993.6294	0.0000	1.0000
F81IG	40	-2957.2935	5999.0255	0.0000	1.0000
F81I	39	-2963.5351	6009.2865	0.0000	1.0000
JC69G	36	-2968.9432	6013.4720	0.0000	1.0000
JC69IG	37	-2971.4961	6020.7820	0.0000	1.0000
JC69I	36	-2977.8282	6031.2418	0.0000	1.0000
F81	38	-3011.9520	6103.9040	0.0000	1.0000
JC69	35	-3026.2796	6125.9463	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2867.4445	5814.8891	0.4868	0.4868
HKYIG	41	-2866.4546	5814.9092	0.4819	0.9687
GTRG	44	-2866.4078	5820.8156	0.0251	0.9939
GTRIG	45	-2866.8901	5823.7802	0.0057	0.9996
HKYI	40	-2874.5491	5829.0982	0.0004	1.0000
GTRI	44	-2874.2111	5836.4222	0.0000	1.0000
K2PG	37	-2885.0252	5844.0504	0.0000	1.0000
K2PIG	38	-2884.1066	5844.2132	0.0000	1.0000
SYMG	41	-2884.8895	5851.7790	0.0000	1.0000
K2PI	37	-2891.8653	5857.7306	0.0000	1.0000
SYMIG	42	-2887.2591	5858.5181	0.0000	1.0000
SYMI	41	-2894.1097	5870.2195	0.0000	1.0000
HKY	39	-2927.7300	5933.4600	0.0000	1.0000
GTR	43	-2926.6550	5939.3100	0.0000	1.0000
K2P	36	-2946.5926	5965.1852	0.0000	1.0000
SYM	40	-2946.4818	5972.9637	0.0000	1.0000
F81G	39	-2955.7066	5989.4132	0.0000	1.0000
F81IG	40	-2957.2935	5994.5870	0.0000	1.0000
F81I	39	-2963.5351	6005.0702	0.0000	1.0000
JC69G	36	-2968.9432	6009.8865	0.0000	1.0000
JC69IG	37	-2971.4961	6016.9922	0.0000	1.0000
JC69I	36	-2977.8282	6027.6564	0.0000	1.0000
F81	38	-3011.9520	6099.9040	0.0000	1.0000
JC69	35	-3026.2796	6122.5592	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2867.4445	6001.2608	0.9110	0.9110
HKYIG	41	-2866.4546	6005.9403	0.0878	0.9987
HKYI	40	-2874.5491	6015.4700	0.0007	0.9995
K2PG	37	-2885.0252	6016.4443	0.0005	1.0000
K2PIG	38	-2884.1066	6021.2663	0.0000	1.0000
GTRG	44	-2866.4078	6025.8246	0.0000	1.0000
K2PI	37	-2891.8653	6030.1245	0.0000	1.0000
GTRIG	45	-2866.8901	6033.4484	0.0000	1.0000
GTRI	44	-2874.2111	6041.4312	0.0000	1.0000
SYMG	41	-2884.8895	6042.8101	0.0000	1.0000
SYMIG	42	-2887.2591	6054.2085	0.0000	1.0000
SYMI	41	-2894.1097	6061.2505	0.0000	1.0000
HKY	39	-2927.7300	6115.1725	0.0000	1.0000
K2P	36	-2946.5926	6132.9198	0.0000	1.0000
GTR	43	-2926.6550	6139.6596	0.0000	1.0000
SYM	40	-2946.4818	6159.3354	0.0000	1.0000
F81G	39	-2955.7066	6171.1257	0.0000	1.0000
JC69G	36	-2968.9432	6177.6211	0.0000	1.0000
F81IG	40	-2957.2935	6180.9588	0.0000	1.0000
F81I	39	-2963.5351	6186.7827	0.0000	1.0000
JC69IG	37	-2971.4961	6189.3861	0.0000	1.0000
JC69I	36	-2977.8282	6195.3910	0.0000	1.0000
F81	38	-3011.9520	6276.9572	0.0000	1.0000
JC69	35	-3026.2796	6285.6345	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_7199.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7199.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/chr4_7199.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7199.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/chr4_7199.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7199.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

