
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:52 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_21254.phylip" (19 taxa, 502 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-1994.1163	4075.3476	0.3206	0.3206
HKYG	40	-1994.4315	4075.9779	0.2339	0.5545
HKYIG	41	-1993.5137	4076.5143	0.1789	0.7334
GTRI	44	-1990.4028	4077.4709	0.1109	0.8443
GTRG	44	-1990.6235	4077.9123	0.0889	0.9332
GTRIG	45	-1989.7024	4078.4838	0.0668	1.0000
HKY	39	-2024.4220	4133.5972	0.0000	1.0000
GTR	43	-2020.7607	4135.7834	0.0000	1.0000
SYMG	41	-2023.1812	4135.8493	0.0000	1.0000
SYMIG	42	-2022.6187	4137.1066	0.0000	1.0000
SYMI	41	-2024.5330	4138.5529	0.0000	1.0000
K2PG	37	-2030.5668	4141.1939	0.0000	1.0000
K2PI	37	-2030.8498	4141.7600	0.0000	1.0000
K2PIG	38	-2031.2023	4144.8063	0.0000	1.0000
SYM	40	-2054.2775	4195.6699	0.0000	1.0000
K2P	36	-2059.2393	4196.2077	0.0000	1.0000
F81I	39	-2098.4713	4281.6958	0.0000	1.0000
F81G	39	-2099.8502	4284.4536	0.0000	1.0000
F81IG	40	-2099.1035	4285.3219	0.0000	1.0000
JC69I	36	-2123.0214	4323.7719	0.0000	1.0000
JC69G	36	-2123.7400	4325.2091	0.0000	1.0000
JC69IG	37	-2122.8006	4325.6616	0.0000	1.0000
F81	38	-2123.8466	4330.0950	0.0000	1.0000
JC69	35	-2148.7708	4372.9493	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1994.1163	4068.2326	0.2320	0.2320
GTRI	44	-1990.4028	4068.8057	0.1742	0.4061
HKYG	40	-1994.4315	4068.8629	0.1692	0.5754
HKYIG	41	-1993.5137	4069.0273	0.1559	0.7313
GTRG	44	-1990.6235	4069.2471	0.1397	0.8709
GTRIG	45	-1989.7024	4069.4049	0.1291	1.0000
HKY	39	-2024.4220	4126.8440	0.0000	1.0000
GTR	43	-2020.7607	4127.5214	0.0000	1.0000
SYMG	41	-2023.1812	4128.3623	0.0000	1.0000
SYMIG	42	-2022.6187	4129.2374	0.0000	1.0000
SYMI	41	-2024.5330	4131.0659	0.0000	1.0000
K2PG	37	-2030.5668	4135.1336	0.0000	1.0000
K2PI	37	-2030.8498	4135.6996	0.0000	1.0000
K2PIG	38	-2031.2023	4138.4046	0.0000	1.0000
SYM	40	-2054.2775	4188.5549	0.0000	1.0000
K2P	36	-2059.2393	4190.4787	0.0000	1.0000
F81I	39	-2098.4713	4274.9425	0.0000	1.0000
F81G	39	-2099.8502	4277.7004	0.0000	1.0000
F81IG	40	-2099.1035	4278.2070	0.0000	1.0000
JC69I	36	-2123.0214	4318.0428	0.0000	1.0000
JC69G	36	-2123.7400	4319.4801	0.0000	1.0000
JC69IG	37	-2122.8006	4319.6012	0.0000	1.0000
F81	38	-2123.8466	4323.6933	0.0000	1.0000
JC69	35	-2148.7708	4367.5416	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1994.1163	4236.9766	0.5520	0.5520
HKYG	40	-1994.4315	4237.6069	0.4028	0.9548
HKYIG	41	-1993.5137	4241.9899	0.0450	0.9998
GTRI	44	-1990.4028	4254.4241	0.0001	0.9999
GTRG	44	-1990.6235	4254.8655	0.0001	1.0000
GTRIG	45	-1989.7024	4259.2419	0.0000	1.0000
K2PG	37	-2030.5668	4291.2218	0.0000	1.0000
HKY	39	-2024.4220	4291.3694	0.0000	1.0000
K2PI	37	-2030.8498	4291.7878	0.0000	1.0000
K2PIG	38	-2031.2023	4298.7114	0.0000	1.0000
SYMG	41	-2023.1812	4301.3249	0.0000	1.0000
SYMI	41	-2024.5330	4304.0285	0.0000	1.0000
SYMIG	42	-2022.6187	4306.4186	0.0000	1.0000
GTR	43	-2020.7607	4308.9212	0.0000	1.0000
K2P	36	-2059.2393	4342.3483	0.0000	1.0000
SYM	40	-2054.2775	4357.2989	0.0000	1.0000
F81I	39	-2098.4713	4439.4679	0.0000	1.0000
F81G	39	-2099.8502	4442.2258	0.0000	1.0000
F81IG	40	-2099.1035	4446.9510	0.0000	1.0000
JC69I	36	-2123.0214	4469.9124	0.0000	1.0000
JC69G	36	-2123.7400	4471.3497	0.0000	1.0000
JC69IG	37	-2122.8006	4475.6894	0.0000	1.0000
F81	38	-2123.8466	4484.0001	0.0000	1.0000
JC69	35	-2148.7708	4515.1926	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip = 1 - 502;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip = 1 - 502;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip = 1 - 502;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21254.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

