
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:26 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/chr5_1701.phylip" (19 taxa, 919 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-4152.2723	8397.0756	0.7291	0.7291
GTRIG	45	-4152.1696	8399.0814	0.2674	0.9966
HKYG	40	-4162.7337	8409.2032	0.0017	0.9983
GTRI	44	-4158.8238	8410.1785	0.0010	0.9993
HKYIG	41	-4162.5631	8411.0533	0.0007	1.0000
SYMG	41	-4166.5353	8418.9977	0.0000	1.0000
HKYI	40	-4167.9607	8419.6572	0.0000	1.0000
SYMIG	42	-4166.3622	8420.8476	0.0000	1.0000
K2PG	37	-4172.8312	8422.8542	0.0000	1.0000
K2PIG	38	-4172.6019	8424.5720	0.0000	1.0000
SYMI	41	-4172.1989	8430.3249	0.0000	1.0000
K2PI	37	-4177.7870	8432.7659	0.0000	1.0000
GTR	43	-4221.8094	8533.9433	0.0000	1.0000
HKY	39	-4229.3769	8540.3033	0.0000	1.0000
SYM	40	-4233.7935	8551.3228	0.0000	1.0000
K2P	36	-4239.1006	8553.2216	0.0000	1.0000
F81G	39	-4302.3367	8686.2229	0.0000	1.0000
F81IG	40	-4302.0499	8687.8355	0.0000	1.0000
JC69G	36	-4308.7233	8692.4670	0.0000	1.0000
F81I	39	-4305.6963	8692.9421	0.0000	1.0000
JC69IG	37	-4308.4702	8694.1321	0.0000	1.0000
JC69I	36	-4312.2291	8699.4785	0.0000	1.0000
F81	38	-4363.3989	8806.1660	0.0000	1.0000
JC69	35	-4369.9053	8812.6644	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4152.2723	8392.5447	0.7085	0.7085
GTRIG	45	-4152.1696	8394.3391	0.2889	0.9974
HKYG	40	-4162.7337	8405.4674	0.0011	0.9985
GTRI	44	-4158.8238	8405.6476	0.0010	0.9995
HKYIG	41	-4162.5631	8407.1262	0.0005	1.0000
SYMG	41	-4166.5353	8415.0707	0.0000	1.0000
HKYI	40	-4167.9607	8415.9215	0.0000	1.0000
SYMIG	42	-4166.3622	8416.7244	0.0000	1.0000
K2PG	37	-4172.8312	8419.6624	0.0000	1.0000
K2PIG	38	-4172.6019	8421.2038	0.0000	1.0000
SYMI	41	-4172.1989	8426.3979	0.0000	1.0000
K2PI	37	-4177.7870	8429.5741	0.0000	1.0000
GTR	43	-4221.8094	8529.6187	0.0000	1.0000
HKY	39	-4229.3769	8536.7538	0.0000	1.0000
SYM	40	-4233.7935	8547.5870	0.0000	1.0000
K2P	36	-4239.1006	8550.2012	0.0000	1.0000
F81G	39	-4302.3367	8682.6734	0.0000	1.0000
F81IG	40	-4302.0499	8684.0998	0.0000	1.0000
F81I	39	-4305.6963	8689.3926	0.0000	1.0000
JC69G	36	-4308.7233	8689.4466	0.0000	1.0000
JC69IG	37	-4308.4702	8690.9403	0.0000	1.0000
JC69I	36	-4312.2291	8696.4581	0.0000	1.0000
F81	38	-4363.3989	8802.7978	0.0000	1.0000
JC69	35	-4369.9053	8809.8105	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-4172.8312	8598.1240	0.5008	0.5008
HKYG	40	-4162.7337	8598.3989	0.4364	0.9372
K2PIG	38	-4172.6019	8604.4887	0.0208	0.9580
GTRG	44	-4152.2723	8604.7692	0.0181	0.9760
HKYIG	41	-4162.5631	8604.8810	0.0171	0.9931
K2PI	37	-4177.7870	8608.0356	0.0035	0.9966
HKYI	40	-4167.9607	8608.8529	0.0023	0.9990
GTRIG	45	-4152.1696	8611.3870	0.0007	0.9996
SYMG	41	-4166.5353	8612.8254	0.0003	1.0000
GTRI	44	-4158.8238	8617.8722	0.0000	1.0000
SYMIG	42	-4166.3622	8619.3024	0.0000	1.0000
SYMI	41	-4172.1989	8624.1526	0.0000	1.0000
K2P	36	-4239.1006	8723.8395	0.0000	1.0000
HKY	39	-4229.3769	8724.8620	0.0000	1.0000
GTR	43	-4221.8094	8737.0200	0.0000	1.0000
SYM	40	-4233.7935	8740.5185	0.0000	1.0000
JC69G	36	-4308.7233	8863.0849	0.0000	1.0000
JC69IG	37	-4308.4702	8869.4019	0.0000	1.0000
JC69I	36	-4312.2291	8870.0964	0.0000	1.0000
F81G	39	-4302.3367	8870.7816	0.0000	1.0000
F81IG	40	-4302.0499	8877.0312	0.0000	1.0000
F81I	39	-4305.6963	8877.5007	0.0000	1.0000
JC69	35	-4369.9053	8978.6255	0.0000	1.0000
F81	38	-4363.3989	8986.0827	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/chr5_1701.phylip = 1 - 919;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1701.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/chr5_1701.phylip = 1 - 919;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1701.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1701.phylip = 1 - 919;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1701.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

