
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:31 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_10160.phylip" (19 taxa, 578 characters)

Minimum AIC  model: GTRG
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	-2048.7805	4183.6689	0.4549	0.4549
GTRG	44	-2044.3839	4184.1974	0.3492	0.8041
GTRIG	45	-2044.3141	4186.4102	0.1155	0.9196
HKYI	40	-2050.9819	4188.0719	0.0503	0.9699
GTRI	44	-2046.8367	4189.1031	0.0301	1.0000
HKYIG	41	-2058.5098	4205.4449	0.0000	1.0000
HKY	39	-2077.8036	4239.4065	0.0000	1.0000
GTR	43	-2073.4621	4240.0102	0.0000	1.0000
K2PG	37	-2097.1951	4273.5976	0.0000	1.0000
K2PI	37	-2099.6150	4278.4374	0.0000	1.0000
SYMG	41	-2096.1697	4280.7648	0.0000	1.0000
SYMI	41	-2098.5868	4285.5989	0.0000	1.0000
F81G	39	-2104.9031	4293.6055	0.0000	1.0000
K2PIG	38	-2107.0388	4295.5766	0.0000	1.0000
F81IG	40	-2104.8611	4295.8302	0.0000	1.0000
F81I	39	-2107.2375	4298.2743	0.0000	1.0000
SYMIG	42	-2105.7424	4302.2361	0.0000	1.0000
K2P	36	-2125.6384	4328.2009	0.0000	1.0000
SYM	40	-2125.0678	4336.2436	0.0000	1.0000
F81	38	-2131.8801	4345.2594	0.0000	1.0000
JC69G	36	-2152.7452	4382.4146	0.0000	1.0000
JC69IG	37	-2152.6963	4384.6001	0.0000	1.0000
JC69I	36	-2154.9869	4386.8981	0.0000	1.0000
JC69	35	-2180.3148	4435.2790	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2044.3839	4176.7678	0.4489	0.4489
HKYG	40	-2048.7805	4177.5609	0.3020	0.7509
GTRIG	45	-2044.3141	4178.6283	0.1771	0.9280
GTRI	44	-2046.8367	4181.6734	0.0386	0.9666
HKYI	40	-2050.9819	4181.9639	0.0334	1.0000
HKYIG	41	-2058.5098	4199.0196	0.0000	1.0000
GTR	43	-2073.4621	4232.9241	0.0000	1.0000
HKY	39	-2077.8036	4233.6072	0.0000	1.0000
K2PG	37	-2097.1951	4268.3902	0.0000	1.0000
K2PI	37	-2099.6150	4273.2300	0.0000	1.0000
SYMG	41	-2096.1697	4274.3394	0.0000	1.0000
SYMI	41	-2098.5868	4279.1735	0.0000	1.0000
F81G	39	-2104.9031	4287.8062	0.0000	1.0000
F81IG	40	-2104.8611	4289.7222	0.0000	1.0000
K2PIG	38	-2107.0388	4290.0775	0.0000	1.0000
F81I	39	-2107.2375	4292.4751	0.0000	1.0000
SYMIG	42	-2105.7424	4295.4847	0.0000	1.0000
K2P	36	-2125.6384	4323.2767	0.0000	1.0000
SYM	40	-2125.0678	4330.1356	0.0000	1.0000
F81	38	-2131.8801	4339.7603	0.0000	1.0000
JC69G	36	-2152.7452	4377.4904	0.0000	1.0000
JC69IG	37	-2152.6963	4379.3927	0.0000	1.0000
JC69I	36	-2154.9869	4381.9739	0.0000	1.0000
JC69	35	-2180.3148	4430.6296	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2048.7805	4351.9439	0.9002	0.9002
HKYI	40	-2050.9819	4356.3469	0.0996	0.9998
GTRG	44	-2044.3839	4368.5891	0.0002	1.0000
GTRI	44	-2046.8367	4373.4947	0.0000	1.0000
GTRIG	45	-2044.3141	4374.8091	0.0000	1.0000
HKYIG	41	-2058.5098	4377.7621	0.0000	1.0000
HKY	39	-2077.8036	4403.6306	0.0000	1.0000
GTR	43	-2073.4621	4420.3858	0.0000	1.0000
K2PG	37	-2097.1951	4429.6944	0.0000	1.0000
K2PI	37	-2099.6150	4434.5343	0.0000	1.0000
SYMG	41	-2096.1697	4453.0819	0.0000	1.0000
K2PIG	38	-2107.0388	4455.7413	0.0000	1.0000
F81G	39	-2104.9031	4457.8296	0.0000	1.0000
SYMI	41	-2098.5868	4457.9160	0.0000	1.0000
F81I	39	-2107.2375	4462.4985	0.0000	1.0000
F81IG	40	-2104.8611	4464.1052	0.0000	1.0000
SYMIG	42	-2105.7424	4478.5868	0.0000	1.0000
K2P	36	-2125.6384	4480.2214	0.0000	1.0000
SYM	40	-2125.0678	4504.5186	0.0000	1.0000
F81	38	-2131.8801	4505.4241	0.0000	1.0000
JC69G	36	-2152.7452	4534.4351	0.0000	1.0000
JC69I	36	-2154.9869	4538.9186	0.0000	1.0000
JC69IG	37	-2152.6963	4540.6969	0.0000	1.0000
JC69	35	-2180.3148	4583.2146	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_10160.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10160.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10160.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10160.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/chr5_10160.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10160.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

