
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:20 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/chrZ_11491.phylip" (19 taxa, 652 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	-1959.5504	4004.4691	0.4565	0.4565
HKYI	40	-1959.9713	4005.3108	0.2997	0.7561
HKYIG	41	-1959.3126	4006.2710	0.1854	0.9415
GTRG	44	-1957.6440	4009.8118	0.0316	0.9731
GTRI	44	-1958.4199	4011.3637	0.0145	0.9876
GTRIG	45	-1957.4266	4011.6850	0.0124	1.0000
K2PG	37	-1978.1247	4034.8292	0.0000	1.0000
K2PI	37	-1978.2341	4035.0479	0.0000	1.0000
K2PIG	38	-1977.8292	4036.4937	0.0000	1.0000
SYMG	41	-1976.9091	4041.4642	0.0000	1.0000
SYMI	41	-1977.0678	4041.7815	0.0000	1.0000
SYMIG	42	-1976.6062	4043.1435	0.0000	1.0000
HKY	39	-1980.2377	4043.5735	0.0000	1.0000
GTR	43	-1978.1273	4048.4784	0.0000	1.0000
K2P	36	-1999.9811	4076.2939	0.0000	1.0000
SYM	40	-1998.8915	4083.1512	0.0000	1.0000
F81G	39	-2007.5864	4098.2708	0.0000	1.0000
F81I	39	-2009.1570	4101.4120	0.0000	1.0000
F81IG	40	-2013.4406	4112.2495	0.0000	1.0000
JC69I	36	-2028.7066	4133.7450	0.0000	1.0000
JC69G	36	-2029.9312	4136.1940	0.0000	1.0000
JC69IG	37	-2029.6908	4137.9614	0.0000	1.0000
F81	38	-2033.4815	4147.7982	0.0000	1.0000
JC69	35	-2050.1405	4174.3718	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1959.5504	3999.1009	0.4238	0.4238
HKYI	40	-1959.9713	3999.9426	0.2782	0.7021
HKYIG	41	-1959.3126	4000.6251	0.1978	0.8998
GTRG	44	-1957.6440	4003.2879	0.0522	0.9521
GTRI	44	-1958.4199	4004.8398	0.0240	0.9761
GTRIG	45	-1957.4266	4004.8533	0.0239	1.0000
K2PG	37	-1978.1247	4030.2494	0.0000	1.0000
K2PI	37	-1978.2341	4030.4681	0.0000	1.0000
K2PIG	38	-1977.8292	4031.6585	0.0000	1.0000
SYMG	41	-1976.9091	4035.8183	0.0000	1.0000
SYMI	41	-1977.0678	4036.1356	0.0000	1.0000
SYMIG	42	-1976.6062	4037.2124	0.0000	1.0000
HKY	39	-1980.2377	4038.4754	0.0000	1.0000
GTR	43	-1978.1273	4042.2547	0.0000	1.0000
K2P	36	-1999.9811	4071.9622	0.0000	1.0000
SYM	40	-1998.8915	4077.7829	0.0000	1.0000
F81G	39	-2007.5864	4093.1728	0.0000	1.0000
F81I	39	-2009.1570	4096.3140	0.0000	1.0000
F81IG	40	-2013.4406	4106.8813	0.0000	1.0000
JC69I	36	-2028.7066	4129.4133	0.0000	1.0000
JC69G	36	-2029.9312	4131.8623	0.0000	1.0000
JC69IG	37	-2029.6908	4133.3816	0.0000	1.0000
F81	38	-2033.4815	4142.9629	0.0000	1.0000
JC69	35	-2050.1405	4170.2809	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1959.5504	4178.3027	0.5860	0.5860
HKYI	40	-1959.9713	4179.1444	0.3847	0.9707
HKYIG	41	-1959.3126	4184.3069	0.0291	0.9998
K2PG	37	-1978.1247	4196.0110	0.0001	0.9999
K2PI	37	-1978.2341	4196.2297	0.0001	1.0000
GTRG	44	-1957.6440	4200.4099	0.0000	1.0000
K2PIG	38	-1977.8292	4201.9002	0.0000	1.0000
GTRI	44	-1958.4199	4201.9618	0.0000	1.0000
GTRIG	45	-1957.4266	4206.4553	0.0000	1.0000
HKY	39	-1980.2377	4213.1972	0.0000	1.0000
SYMG	41	-1976.9091	4219.5001	0.0000	1.0000
SYMI	41	-1977.0678	4219.8174	0.0000	1.0000
SYMIG	42	-1976.6062	4225.3743	0.0000	1.0000
K2P	36	-1999.9811	4233.2438	0.0000	1.0000
GTR	43	-1978.1273	4234.8966	0.0000	1.0000
SYM	40	-1998.8915	4256.9847	0.0000	1.0000
F81G	39	-2007.5864	4267.8945	0.0000	1.0000
F81I	39	-2009.1570	4271.0357	0.0000	1.0000
F81IG	40	-2013.4406	4286.0831	0.0000	1.0000
JC69I	36	-2028.7066	4290.6949	0.0000	1.0000
JC69G	36	-2029.9312	4293.1439	0.0000	1.0000
JC69IG	37	-2029.6908	4299.1432	0.0000	1.0000
F81	38	-2033.4815	4313.2046	0.0000	1.0000
JC69	35	-2050.1405	4327.0825	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/chrZ_11491.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11491.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/chrZ_11491.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11491.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/chrZ_11491.phylip = 1 - 652;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11491.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

