
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:32 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/chr18_3123.phylip" (19 taxa, 1069 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	-4098.4060	8288.6793	0.5709	0.5709
GTRIG	45	-4098.0645	8290.1760	0.2701	0.8411
GTRI	44	-4100.1978	8292.2627	0.0952	0.9362
HKYG	40	-4105.6072	8294.4051	0.0326	0.9688
HKYIG	41	-4105.1973	8295.7480	0.0167	0.9855
HKYI	40	-4106.4181	8296.0268	0.0145	1.0000
K2PG	37	-4140.6323	8357.9920	0.0000	1.0000
K2PI	37	-4140.9308	8358.5891	0.0000	1.0000
K2PIG	38	-4140.1340	8359.1456	0.0000	1.0000
SYMG	41	-4140.0576	8365.4687	0.0000	1.0000
SYMI	41	-4140.2300	8365.8134	0.0000	1.0000
SYMIG	42	-4139.4735	8366.4675	0.0000	1.0000
HKY	39	-4175.8621	8432.7563	0.0000	1.0000
GTR	43	-4172.5319	8434.7556	0.0000	1.0000
F81I	39	-4197.3650	8475.7620	0.0000	1.0000
F81IG	40	-4196.9124	8477.0154	0.0000	1.0000
F81G	39	-4199.1506	8479.3332	0.0000	1.0000
K2P	36	-4208.2119	8491.0052	0.0000	1.0000
SYM	40	-4207.8064	8498.8035	0.0000	1.0000
JC69G	36	-4223.0842	8520.7498	0.0000	1.0000
JC69I	36	-4225.0648	8524.7109	0.0000	1.0000
JC69IG	37	-4224.2645	8525.2564	0.0000	1.0000
F81	38	-4259.7990	8598.4756	0.0000	1.0000
JC69	35	-4284.3396	8641.1187	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4098.4060	8284.8121	0.5664	0.5664
GTRIG	45	-4098.0645	8286.1291	0.2932	0.8595
GTRI	44	-4100.1978	8288.3955	0.0944	0.9539
HKYG	40	-4105.6072	8291.2144	0.0231	0.9770
HKYIG	41	-4105.1973	8292.3945	0.0128	0.9898
HKYI	40	-4106.4181	8292.8361	0.0102	1.0000
K2PG	37	-4140.6323	8355.2645	0.0000	1.0000
K2PI	37	-4140.9308	8355.8617	0.0000	1.0000
K2PIG	38	-4140.1340	8356.2680	0.0000	1.0000
SYMG	41	-4140.0576	8362.1153	0.0000	1.0000
SYMI	41	-4140.2300	8362.4600	0.0000	1.0000
SYMIG	42	-4139.4735	8362.9471	0.0000	1.0000
HKY	39	-4175.8621	8429.7243	0.0000	1.0000
GTR	43	-4172.5319	8431.0639	0.0000	1.0000
F81I	39	-4197.3650	8472.7299	0.0000	1.0000
F81IG	40	-4196.9124	8473.8247	0.0000	1.0000
F81G	39	-4199.1506	8476.3012	0.0000	1.0000
K2P	36	-4208.2119	8488.4238	0.0000	1.0000
SYM	40	-4207.8064	8495.6128	0.0000	1.0000
JC69G	36	-4223.0842	8518.1684	0.0000	1.0000
JC69I	36	-4225.0648	8522.1295	0.0000	1.0000
JC69IG	37	-4224.2645	8522.5289	0.0000	1.0000
F81	38	-4259.7990	8595.5979	0.0000	1.0000
JC69	35	-4284.3396	8638.6792	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4105.6072	8490.1936	0.6702	0.6702
HKYI	40	-4106.4181	8491.8153	0.2979	0.9682
HKYIG	41	-4105.1973	8496.3482	0.0309	0.9990
GTRG	44	-4098.4060	8503.6892	0.0008	0.9998
GTRI	44	-4100.1978	8507.2726	0.0001	1.0000
GTRIG	45	-4098.0645	8509.9806	0.0000	1.0000
K2PG	37	-4140.6323	8539.3202	0.0000	1.0000
K2PI	37	-4140.9308	8539.9174	0.0000	1.0000
K2PIG	38	-4140.1340	8545.2982	0.0000	1.0000
SYMG	41	-4140.0576	8566.0689	0.0000	1.0000
SYMI	41	-4140.2300	8566.4136	0.0000	1.0000
SYMIG	42	-4139.4735	8571.8752	0.0000	1.0000
HKY	39	-4175.8621	8623.7289	0.0000	1.0000
GTR	43	-4172.5319	8644.9665	0.0000	1.0000
F81I	39	-4197.3650	8666.7346	0.0000	1.0000
K2P	36	-4208.2119	8667.5050	0.0000	1.0000
F81G	39	-4199.1506	8670.3059	0.0000	1.0000
F81IG	40	-4196.9124	8672.8039	0.0000	1.0000
SYM	40	-4207.8064	8694.5920	0.0000	1.0000
JC69G	36	-4223.0842	8697.2496	0.0000	1.0000
JC69I	36	-4225.0648	8701.2108	0.0000	1.0000
JC69IG	37	-4224.2645	8706.5847	0.0000	1.0000
F81	38	-4259.7990	8784.6281	0.0000	1.0000
JC69	35	-4284.3396	8812.7859	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/chr18_3123.phylip = 1 - 1069;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_3123.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/chr18_3123.phylip = 1 - 1069;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_3123.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/chr18_3123.phylip = 1 - 1069;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr18_3123.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

