
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:57 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/chr8_4241.phylip" (19 taxa, 742 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	-2845.4882	5784.6578	0.4494	0.4494
GTRIG	45	-2844.5304	5785.0090	0.3771	0.8265
HKYG	40	-2851.5636	5787.8062	0.0931	0.9196
HKYIG	41	-2850.5954	5788.1107	0.0800	0.9996
GTRI	44	-2852.7399	5799.1614	0.0003	0.9999
HKYI	40	-2858.3565	5801.3919	0.0001	1.0000
K2PG	37	-2870.2841	5818.5625	0.0000	1.0000
K2PIG	38	-2869.3906	5818.9973	0.0000	1.0000
SYMG	41	-2868.8865	5824.6929	0.0000	1.0000
SYMIG	42	-2868.0563	5825.2800	0.0000	1.0000
K2PI	37	-2876.1541	5830.3026	0.0000	1.0000
SYMI	41	-2874.4426	5835.8051	0.0000	1.0000
F81G	39	-2908.8022	5900.0489	0.0000	1.0000
F81IG	40	-2908.1283	5900.9357	0.0000	1.0000
F81I	39	-2914.0176	5910.4796	0.0000	1.0000
GTR	43	-2910.2052	5911.8317	0.0000	1.0000
HKY	39	-2917.1624	5916.7692	0.0000	1.0000
JC69G	36	-2924.0547	5923.8880	0.0000	1.0000
JC69IG	37	-2923.4147	5924.8237	0.0000	1.0000
JC69I	36	-2928.9339	5933.6466	0.0000	1.0000
K2P	36	-2936.5837	5948.9462	0.0000	1.0000
SYM	40	-2934.2389	5953.1568	0.0000	1.0000
F81	38	-2971.7325	6023.6813	0.0000	1.0000
JC69	35	-2987.5790	6048.7274	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2845.4882	5778.9763	0.4532	0.4532
GTRIG	45	-2844.5304	5779.0608	0.4345	0.8876
HKYG	40	-2851.5636	5783.1271	0.0569	0.9445
HKYIG	41	-2850.5954	5783.1907	0.0551	0.9996
GTRI	44	-2852.7399	5793.4799	0.0003	0.9999
HKYI	40	-2858.3565	5796.7129	0.0001	1.0000
K2PG	37	-2870.2841	5814.5681	0.0000	1.0000
K2PIG	38	-2869.3906	5814.7811	0.0000	1.0000
SYMG	41	-2868.8865	5819.7729	0.0000	1.0000
SYMIG	42	-2868.0563	5820.1127	0.0000	1.0000
K2PI	37	-2876.1541	5826.3082	0.0000	1.0000
SYMI	41	-2874.4426	5830.8851	0.0000	1.0000
F81G	39	-2908.8022	5895.6045	0.0000	1.0000
F81IG	40	-2908.1283	5896.2566	0.0000	1.0000
F81I	39	-2914.0176	5906.0352	0.0000	1.0000
GTR	43	-2910.2052	5906.4105	0.0000	1.0000
HKY	39	-2917.1624	5912.3247	0.0000	1.0000
JC69G	36	-2924.0547	5920.1093	0.0000	1.0000
JC69IG	37	-2923.4147	5920.8294	0.0000	1.0000
JC69I	36	-2928.9339	5929.8679	0.0000	1.0000
K2P	36	-2936.5837	5945.1675	0.0000	1.0000
SYM	40	-2934.2389	5948.4778	0.0000	1.0000
F81	38	-2971.7325	6019.4650	0.0000	1.0000
JC69	35	-2987.5790	6045.1580	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2851.5636	5967.5011	0.9101	0.9101
HKYIG	41	-2850.5954	5972.1740	0.0880	0.9980
HKYI	40	-2858.3565	5981.0869	0.0010	0.9991
GTRG	44	-2845.4882	5981.7877	0.0007	0.9998
K2PG	37	-2870.2841	5985.1141	0.0001	0.9999
GTRIG	45	-2844.5304	5986.4815	0.0001	1.0000
K2PIG	38	-2869.3906	5989.9364	0.0000	1.0000
GTRI	44	-2852.7399	5996.2912	0.0000	1.0000
K2PI	37	-2876.1541	5996.8542	0.0000	1.0000
SYMG	41	-2868.8865	6008.7563	0.0000	1.0000
SYMIG	42	-2868.0563	6013.7053	0.0000	1.0000
SYMI	41	-2874.4426	6019.8684	0.0000	1.0000
F81G	39	-2908.8022	6075.3691	0.0000	1.0000
F81IG	40	-2908.1283	6080.6306	0.0000	1.0000
F81I	39	-2914.0176	6085.7998	0.0000	1.0000
JC69G	36	-2924.0547	6086.0459	0.0000	1.0000
JC69IG	37	-2923.4147	6091.3753	0.0000	1.0000
HKY	39	-2917.1624	6092.0894	0.0000	1.0000
JC69I	36	-2928.9339	6095.8045	0.0000	1.0000
GTR	43	-2910.2052	6104.6125	0.0000	1.0000
K2P	36	-2936.5837	6111.1041	0.0000	1.0000
SYM	40	-2934.2389	6132.8517	0.0000	1.0000
F81	38	-2971.7325	6194.6203	0.0000	1.0000
JC69	35	-2987.5790	6206.4852	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/chr8_4241.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4241.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/chr8_4241.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4241.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/chr8_4241.phylip = 1 - 742;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4241.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

