
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:15 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/chr4_7570.phylip" (19 taxa, 672 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	-1917.8154	3920.8288	0.4550	0.4550
HKYI	40	-1918.3878	3921.9737	0.2567	0.7117
HKYIG	41	-1917.6249	3922.7165	0.1771	0.8888
GTRG	44	-1915.3095	3924.9348	0.0584	0.9472
GTRI	44	-1915.9580	3926.2317	0.0305	0.9777
GTRIG	45	-1915.1415	3926.8964	0.0219	0.9996
K2PG	37	-1929.6432	3937.7218	0.0001	0.9997
SYMG	41	-1925.1294	3937.7254	0.0001	0.9998
K2PI	37	-1930.1249	3938.6851	0.0001	0.9999
SYMI	41	-1925.7941	3939.0549	0.0001	0.9999
K2PIG	38	-1929.4782	3939.6389	0.0000	1.0000
SYMIG	42	-1924.9509	3939.6442	0.0000	1.0000
HKY	39	-1939.4113	3961.7593	0.0000	1.0000
GTR	43	-1935.9649	3963.9552	0.0000	1.0000
SYM	40	-1945.4717	3976.1416	0.0000	1.0000
K2P	36	-1951.3593	3978.9138	0.0000	1.0000
F81G	39	-1950.0743	3983.0852	0.0000	1.0000
F81I	39	-1950.4909	3983.9186	0.0000	1.0000
F81IG	40	-1949.9568	3985.1116	0.0000	1.0000
JC69G	36	-1964.1255	4004.4464	0.0000	1.0000
JC69I	36	-1964.4983	4005.1919	0.0000	1.0000
JC69IG	37	-1964.0461	4006.5276	0.0000	1.0000
F81	38	-1971.0650	4022.8124	0.0000	1.0000
JC69	35	-1984.2687	4042.4997	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1917.8154	3915.6307	0.4083	0.4083
HKYI	40	-1918.3878	3916.7756	0.2303	0.6386
HKYIG	41	-1917.6249	3917.2498	0.1817	0.8203
GTRG	44	-1915.3095	3918.6190	0.0916	0.9119
GTRI	44	-1915.9580	3919.9160	0.0479	0.9598
GTRIG	45	-1915.1415	3920.2830	0.0399	0.9997
SYMG	41	-1925.1294	3932.2587	0.0001	0.9998
K2PG	37	-1929.6432	3933.2865	0.0001	0.9998
SYMI	41	-1925.7941	3933.5882	0.0001	0.9999
SYMIG	42	-1924.9509	3933.9018	0.0000	0.9999
K2PI	37	-1930.1249	3934.2498	0.0000	1.0000
K2PIG	38	-1929.4782	3934.9565	0.0000	1.0000
HKY	39	-1939.4113	3956.8226	0.0000	1.0000
GTR	43	-1935.9649	3957.9297	0.0000	1.0000
SYM	40	-1945.4717	3970.9435	0.0000	1.0000
K2P	36	-1951.3593	3974.7186	0.0000	1.0000
F81G	39	-1950.0743	3978.1485	0.0000	1.0000
F81I	39	-1950.4909	3978.9819	0.0000	1.0000
F81IG	40	-1949.9568	3979.9135	0.0000	1.0000
JC69G	36	-1964.1255	4000.2511	0.0000	1.0000
JC69I	36	-1964.4983	4000.9966	0.0000	1.0000
JC69IG	37	-1964.0461	4002.0922	0.0000	1.0000
F81	38	-1971.0650	4018.1300	0.0000	1.0000
JC69	35	-1984.2687	4038.5374	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1917.8154	4096.0411	0.5487	0.5487
HKYI	40	-1918.3878	4097.1860	0.3096	0.8583
K2PG	37	-1929.6432	4100.1660	0.0698	0.9281
K2PI	37	-1930.1249	4101.1293	0.0431	0.9712
HKYIG	41	-1917.6249	4102.1704	0.0256	0.9968
K2PIG	38	-1929.4782	4106.3463	0.0032	1.0000
GTRG	44	-1915.3095	4117.0704	0.0000	1.0000
SYMG	41	-1925.1294	4117.1793	0.0000	1.0000
GTRI	44	-1915.9580	4118.3673	0.0000	1.0000
SYMI	41	-1925.7941	4118.5088	0.0000	1.0000
GTRIG	45	-1915.1415	4123.2446	0.0000	1.0000
SYMIG	42	-1924.9509	4123.3326	0.0000	1.0000
HKY	39	-1939.4113	4132.7227	0.0000	1.0000
K2P	36	-1951.3593	4137.0879	0.0000	1.0000
SYM	40	-1945.4717	4151.3538	0.0000	1.0000
GTR	43	-1935.9649	4151.8708	0.0000	1.0000
F81G	39	-1950.0743	4154.0486	0.0000	1.0000
F81I	39	-1950.4909	4154.8820	0.0000	1.0000
F81IG	40	-1949.9568	4160.3239	0.0000	1.0000
JC69G	36	-1964.1255	4162.6204	0.0000	1.0000
JC69I	36	-1964.4983	4163.3659	0.0000	1.0000
JC69IG	37	-1964.0461	4168.9718	0.0000	1.0000
F81	38	-1971.0650	4189.5198	0.0000	1.0000
JC69	35	-1984.2687	4196.3965	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/chr4_7570.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7570.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/chr4_7570.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7570.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/chr4_7570.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7570.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

