
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:06 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/chr2_21462.phylip" (19 taxa, 558 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	-1954.3544	4004.4281	0.4128	0.4128
HKYG	40	-1959.5843	4005.5129	0.2400	0.6527
GTRIG	45	-1954.3244	4006.7347	0.1303	0.7830
GTRI	44	-1955.7487	4007.2166	0.1024	0.8853
HKYIG	41	-1959.5662	4007.8067	0.0762	0.9616
HKYI	40	-1961.4156	4009.1756	0.0384	1.0000
GTR	43	-1967.7057	4028.7732	0.0000	1.0000
HKY	39	-1973.2806	4030.5844	0.0000	1.0000
K2PG	37	-1984.9100	4049.2278	0.0000	1.0000
K2PIG	38	-1984.8798	4051.4706	0.0000	1.0000
SYMG	41	-1981.5435	4051.7614	0.0000	1.0000
K2PI	37	-1986.6842	4052.7762	0.0000	1.0000
SYMIG	42	-1981.5014	4054.0165	0.0000	1.0000
SYMI	41	-1983.0535	4054.7813	0.0000	1.0000
K2P	36	-1999.8613	4076.8359	0.0000	1.0000
SYM	40	-1996.2888	4078.9219	0.0000	1.0000
F81G	39	-2050.6035	4185.2302	0.0000	1.0000
F81IG	40	-2050.5927	4187.5297	0.0000	1.0000
F81I	39	-2052.2747	4188.5725	0.0000	1.0000
F81	38	-2063.2058	4208.1225	0.0000	1.0000
JC69G	36	-2069.0007	4215.1147	0.0000	1.0000
JC69IG	37	-2068.9857	4217.3790	0.0000	1.0000
JC69I	36	-2070.6584	4218.4301	0.0000	1.0000
JC69	35	-2082.2885	4239.4046	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1954.3544	3996.7088	0.4817	0.4817
GTRIG	45	-1954.3244	3998.6487	0.1826	0.6644
HKYG	40	-1959.5843	3999.1686	0.1408	0.8052
GTRI	44	-1955.7487	3999.4973	0.1195	0.9247
HKYIG	41	-1959.5662	4001.1323	0.0528	0.9774
HKYI	40	-1961.4156	4002.8313	0.0226	1.0000
GTR	43	-1967.7057	4021.4113	0.0000	1.0000
HKY	39	-1973.2806	4024.5612	0.0000	1.0000
K2PG	37	-1984.9100	4043.8201	0.0000	1.0000
SYMG	41	-1981.5435	4045.0869	0.0000	1.0000
K2PIG	38	-1984.8798	4045.7596	0.0000	1.0000
SYMIG	42	-1981.5014	4047.0029	0.0000	1.0000
K2PI	37	-1986.6842	4047.3685	0.0000	1.0000
SYMI	41	-1983.0535	4048.1069	0.0000	1.0000
K2P	36	-1999.8613	4071.7226	0.0000	1.0000
SYM	40	-1996.2888	4072.5776	0.0000	1.0000
F81G	39	-2050.6035	4179.2070	0.0000	1.0000
F81IG	40	-2050.5927	4181.1854	0.0000	1.0000
F81I	39	-2052.2747	4182.5493	0.0000	1.0000
F81	38	-2063.2058	4202.4116	0.0000	1.0000
JC69G	36	-2069.0007	4210.0015	0.0000	1.0000
JC69IG	37	-2068.9857	4211.9713	0.0000	1.0000
JC69I	36	-2070.6584	4213.3169	0.0000	1.0000
JC69	35	-2082.2885	4234.5770	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1959.5843	4172.1430	0.8305	0.8305
HKYI	40	-1961.4156	4175.8056	0.1330	0.9635
HKYIG	41	-1959.5662	4178.4310	0.0358	0.9993
GTRG	44	-1954.3544	4186.9806	0.0005	0.9998
GTRI	44	-1955.7487	4189.7691	0.0001	1.0000
HKY	39	-1973.2806	4193.2112	0.0000	1.0000
GTRIG	45	-1954.3244	4193.2449	0.0000	1.0000
K2PG	37	-1984.9100	4203.8214	0.0000	1.0000
GTR	43	-1967.7057	4207.3587	0.0000	1.0000
K2PI	37	-1986.6842	4207.3698	0.0000	1.0000
K2PIG	38	-1984.8798	4210.0853	0.0000	1.0000
SYMG	41	-1981.5435	4222.3857	0.0000	1.0000
SYMI	41	-1983.0535	4225.4056	0.0000	1.0000
K2P	36	-1999.8613	4227.3995	0.0000	1.0000
SYMIG	42	-1981.5014	4228.6260	0.0000	1.0000
SYM	40	-1996.2888	4245.5519	0.0000	1.0000
F81G	39	-2050.6035	4347.8570	0.0000	1.0000
F81I	39	-2052.2747	4351.1993	0.0000	1.0000
F81IG	40	-2050.5927	4354.1598	0.0000	1.0000
JC69G	36	-2069.0007	4365.6784	0.0000	1.0000
F81	38	-2063.2058	4366.7372	0.0000	1.0000
JC69I	36	-2070.6584	4368.9938	0.0000	1.0000
JC69IG	37	-2068.9857	4371.9726	0.0000	1.0000
JC69	35	-2082.2885	4385.9295	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/chr2_21462.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21462.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/chr2_21462.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21462.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/chr2_21462.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21462.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

