
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:55 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_27294.phylip" (19 taxa, 393 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-921.6445	1935.1009	0.4459	0.4459
HKYI	40	-923.4511	1936.2204	0.2548	0.7007
HKYG	40	-923.5624	1936.4430	0.2280	0.9287
GTRIG	45	-919.2207	1940.3723	0.0320	0.9607
GTRI	44	-920.8527	1941.0846	0.0224	0.9830
GTRG	44	-921.1298	1941.6389	0.0170	1.0000
HKY	39	-942.8931	1972.6246	0.0000	1.0000
GTR	43	-940.2404	1977.3233	0.0000	1.0000
K2PIG	38	-948.6160	1981.6049	0.0000	1.0000
K2PI	37	-950.9655	1983.8521	0.0000	1.0000
K2PG	37	-951.4512	1984.8234	0.0000	1.0000
SYMIG	42	-945.5103	1985.3407	0.0000	1.0000
F81IG	40	-948.3126	1985.9433	0.0000	1.0000
F81G	39	-950.3090	1987.4566	0.0000	1.0000
F81I	39	-950.3520	1987.5425	0.0000	1.0000
SYMI	41	-948.0248	1987.8616	0.0000	1.0000
SYMG	41	-948.5701	1988.9521	0.0000	1.0000
K2P	36	-970.9119	2021.3070	0.0000	1.0000
F81	38	-968.7120	2021.7969	0.0000	1.0000
SYM	40	-968.2725	2025.8631	0.0000	1.0000
JC69IG	37	-973.2353	2028.3918	0.0000	1.0000
JC69I	36	-975.5574	2030.5979	0.0000	1.0000
JC69G	36	-975.8491	2031.1814	0.0000	1.0000
JC69	35	-994.5468	2066.1525	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-921.6445	1925.2889	0.4453	0.4453
HKYI	40	-923.4511	1926.9022	0.1988	0.6441
HKYG	40	-923.5624	1927.1248	0.1778	0.8219
GTRIG	45	-919.2207	1928.4414	0.0921	0.9140
GTRI	44	-920.8527	1929.7053	0.0489	0.9629
GTRG	44	-921.1298	1930.2596	0.0371	1.0000
HKY	39	-942.8931	1963.7861	0.0000	1.0000
GTR	43	-940.2404	1966.4809	0.0000	1.0000
K2PIG	38	-948.6160	1973.2320	0.0000	1.0000
SYMIG	42	-945.5103	1975.0207	0.0000	1.0000
K2PI	37	-950.9655	1975.9310	0.0000	1.0000
F81IG	40	-948.3126	1976.6251	0.0000	1.0000
K2PG	37	-951.4512	1976.9023	0.0000	1.0000
SYMI	41	-948.0248	1978.0496	0.0000	1.0000
F81G	39	-950.3090	1978.6181	0.0000	1.0000
F81I	39	-950.3520	1978.7039	0.0000	1.0000
SYMG	41	-948.5701	1979.1401	0.0000	1.0000
F81	38	-968.7120	2013.4240	0.0000	1.0000
K2P	36	-970.9119	2013.8239	0.0000	1.0000
SYM	40	-968.2725	2016.5449	0.0000	1.0000
JC69IG	37	-973.2353	2020.4706	0.0000	1.0000
JC69I	36	-975.5574	2023.1148	0.0000	1.0000
JC69G	36	-975.8491	2023.6982	0.0000	1.0000
JC69	35	-994.5468	2059.0937	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-923.4511	2085.8546	0.4541	0.4541
HKYG	40	-923.5624	2086.0772	0.4063	0.8604
HKYIG	41	-921.6445	2088.2151	0.1395	0.9999
GTRI	44	-920.8527	2104.5529	0.0000	1.0000
GTRG	44	-921.1298	2105.1072	0.0000	1.0000
GTRIG	45	-919.2207	2107.2629	0.0000	1.0000
HKY	39	-942.8931	2118.7647	0.0000	1.0000
K2PI	37	-950.9655	2122.9619	0.0000	1.0000
K2PG	37	-951.4512	2123.9333	0.0000	1.0000
K2PIG	38	-948.6160	2124.2368	0.0000	1.0000
F81G	39	-950.3090	2133.5967	0.0000	1.0000
F81I	39	-950.3520	2133.6825	0.0000	1.0000
F81IG	40	-948.3126	2135.5775	0.0000	1.0000
GTR	43	-940.2404	2137.3547	0.0000	1.0000
SYMI	41	-948.0248	2140.9758	0.0000	1.0000
SYMIG	42	-945.5103	2141.9207	0.0000	1.0000
SYMG	41	-948.5701	2142.0663	0.0000	1.0000
K2P	36	-970.9119	2156.8810	0.0000	1.0000
F81	38	-968.7120	2164.4288	0.0000	1.0000
JC69I	36	-975.5574	2166.1719	0.0000	1.0000
JC69G	36	-975.8491	2166.7554	0.0000	1.0000
JC69IG	37	-973.2353	2167.5016	0.0000	1.0000
SYM	40	-968.2725	2175.4973	0.0000	1.0000
JC69	35	-994.5468	2198.1770	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27294.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27294.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27294.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27294.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) 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_27294.phylip = 1 - 393;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27294.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

