
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:01 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_7959.phylip" (19 taxa, 990 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-4928.5349	9949.2602	0.3290	0.3290
GTRIG	45	-4927.6772	9949.7399	0.2588	0.5878
SYMG	41	-4932.2042	9950.0414	0.2226	0.8104
SYMIG	42	-4931.2762	9950.3666	0.1892	0.9996
SYMI	41	-4939.8519	9965.3367	0.0001	0.9997
GTRI	44	-4936.5861	9965.3627	0.0001	0.9998
K2PIG	38	-4943.8519	9966.8205	0.0001	0.9999
K2PG	37	-4944.9488	9966.8514	0.0000	0.9999
HKYIG	41	-4940.9300	9967.4930	0.0000	1.0000
HKYG	40	-4942.0508	9967.5578	0.0000	1.0000
K2PI	37	-4951.5864	9980.1267	0.0000	1.0000
HKYI	40	-4948.6415	9980.7393	0.0000	1.0000
GTR	43	-4988.5616	10067.1232	0.0000	1.0000
SYM	40	-4991.9319	10067.3200	0.0000	1.0000
K2P	36	-5002.4798	10079.7551	0.0000	1.0000
HKY	39	-4999.5331	10080.3504	0.0000	1.0000
F81IG	40	-5045.7062	10174.8687	0.0000	1.0000
F81G	39	-5047.2009	10175.6860	0.0000	1.0000
JC69IG	37	-5051.4654	10179.8846	0.0000	1.0000
JC69G	36	-5052.8944	10180.5843	0.0000	1.0000
F81I	39	-5050.9008	10183.0858	0.0000	1.0000
JC69I	36	-5056.8420	10188.4793	0.0000	1.0000
F81	38	-5097.2967	10273.7101	0.0000	1.0000
JC69	35	-5103.7412	10280.1240	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4928.5349	9945.0698	0.3500	0.3500
GTRIG	45	-4927.6772	9945.3543	0.3036	0.6537
SYMG	41	-4932.2042	9946.4084	0.1792	0.8329
SYMIG	42	-4931.2762	9946.5525	0.1668	0.9997
GTRI	44	-4936.5861	9961.1723	0.0001	0.9998
SYMI	41	-4939.8519	9961.7037	0.0001	0.9999
K2PIG	38	-4943.8519	9963.7037	0.0000	0.9999
HKYIG	41	-4940.9300	9963.8601	0.0000	0.9999
K2PG	37	-4944.9488	9963.8976	0.0000	1.0000
HKYG	40	-4942.0508	9964.1015	0.0000	1.0000
K2PI	37	-4951.5864	9977.1729	0.0000	1.0000
HKYI	40	-4948.6415	9977.2830	0.0000	1.0000
GTR	43	-4988.5616	10063.1232	0.0000	1.0000
SYM	40	-4991.9319	10063.8638	0.0000	1.0000
K2P	36	-5002.4798	10076.9597	0.0000	1.0000
HKY	39	-4999.5331	10077.0661	0.0000	1.0000
F81IG	40	-5045.7062	10171.4124	0.0000	1.0000
F81G	39	-5047.2009	10172.4018	0.0000	1.0000
JC69IG	37	-5051.4654	10176.9309	0.0000	1.0000
JC69G	36	-5052.8944	10177.7889	0.0000	1.0000
F81I	39	-5050.9008	10179.8016	0.0000	1.0000
JC69I	36	-5056.8420	10185.6839	0.0000	1.0000
F81	38	-5097.2967	10270.5934	0.0000	1.0000
JC69	35	-5103.7412	10277.4825	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-4944.9488	10145.1127	0.6777	0.6777
SYMG	41	-4932.2042	10147.2143	0.2370	0.9147
K2PIG	38	-4943.8519	10149.8165	0.0645	0.9792
SYMIG	42	-4931.2762	10152.2561	0.0190	0.9982
K2PI	37	-4951.5864	10158.3880	0.0009	0.9991
HKYG	40	-4942.0508	10160.0097	0.0004	0.9995
GTRG	44	-4928.5349	10160.5688	0.0003	0.9998
SYMI	41	-4939.8519	10162.5096	0.0001	0.9999
HKYIG	41	-4940.9300	10164.6660	0.0000	1.0000
GTRIG	45	-4927.6772	10165.7510	0.0000	1.0000
HKYI	40	-4948.6415	10173.1912	0.0000	1.0000
GTRI	44	-4936.5861	10176.6713	0.0000	1.0000
K2P	36	-5002.4798	10253.2771	0.0000	1.0000
SYM	40	-4991.9319	10259.7720	0.0000	1.0000
HKY	39	-4999.5331	10268.0766	0.0000	1.0000
GTR	43	-4988.5616	10273.7245	0.0000	1.0000
JC69G	36	-5052.8944	10354.1063	0.0000	1.0000
JC69IG	37	-5051.4654	10358.1459	0.0000	1.0000
JC69I	36	-5056.8420	10362.0013	0.0000	1.0000
F81G	39	-5047.2009	10363.4123	0.0000	1.0000
F81IG	40	-5045.7062	10367.3206	0.0000	1.0000
F81I	39	-5050.9008	10370.8121	0.0000	1.0000
JC69	35	-5103.7412	10448.9021	0.0000	1.0000
F81	38	-5097.2967	10456.7061	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_7959.phylip = 1 - 990;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7959.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_7959.phylip = 1 - 990;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7959.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7959.phylip = 1 - 990;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7959.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


-------------------------------------------------------------
End of Output

