
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:06 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/chr1_32246.phylip" (19 taxa, 752 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1815.6999	3727.2638	0.3036	0.3036
GTRG	44	-1816.8523	3727.3058	0.2973	0.6009
GTRI	44	-1817.2445	3728.0902	0.2009	0.8018
HKYG	40	-1822.7653	3730.1439	0.0719	0.8737
HKYI	40	-1822.8349	3730.2830	0.0671	0.9408
HKYIG	41	-1821.8422	3730.5351	0.0592	1.0000
HKY	39	-1847.0410	3776.4640	0.0000	1.0000
GTR	43	-1842.7381	3776.8208	0.0000	1.0000
SYMG	41	-1849.7151	3786.2810	0.0000	1.0000
SYMIG	42	-1848.6664	3786.4273	0.0000	1.0000
SYMI	41	-1850.2380	3787.3267	0.0000	1.0000
K2PG	37	-1858.3339	3794.6062	0.0000	1.0000
K2PI	37	-1858.6600	3795.2583	0.0000	1.0000
K2PIG	38	-1857.5944	3795.3460	0.0000	1.0000
F81IG	40	-1858.7422	3802.0976	0.0000	1.0000
F81G	39	-1859.9172	3802.2165	0.0000	1.0000
F81I	39	-1860.2423	3802.8667	0.0000	1.0000
SYM	40	-1874.5306	3833.6744	0.0000	1.0000
K2P	36	-1882.0111	3839.7480	0.0000	1.0000
F81	38	-1882.5832	3845.3235	0.0000	1.0000
JC69G	36	-1891.3162	3858.3582	0.0000	1.0000
JC69IG	37	-1890.3350	3858.6085	0.0000	1.0000
JC69I	36	-1891.8528	3859.4315	0.0000	1.0000
JC69	35	-1913.9053	3901.3302	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1815.6999	3721.3998	0.3570	0.3570
GTRG	44	-1816.8523	3721.7047	0.3065	0.6635
GTRI	44	-1817.2445	3722.4891	0.2071	0.8706
HKYG	40	-1822.7653	3725.5307	0.0453	0.9159
HKYI	40	-1822.8349	3725.6698	0.0422	0.9581
HKYIG	41	-1821.8422	3725.6844	0.0419	1.0000
GTR	43	-1842.7381	3771.4761	0.0000	1.0000
HKY	39	-1847.0410	3772.0820	0.0000	1.0000
SYMIG	42	-1848.6664	3781.3328	0.0000	1.0000
SYMG	41	-1849.7151	3781.4303	0.0000	1.0000
SYMI	41	-1850.2380	3782.4760	0.0000	1.0000
K2PG	37	-1858.3339	3790.6678	0.0000	1.0000
K2PIG	38	-1857.5944	3791.1889	0.0000	1.0000
K2PI	37	-1858.6600	3791.3199	0.0000	1.0000
F81IG	40	-1858.7422	3797.4844	0.0000	1.0000
F81G	39	-1859.9172	3797.8344	0.0000	1.0000
F81I	39	-1860.2423	3798.4846	0.0000	1.0000
SYM	40	-1874.5306	3829.0612	0.0000	1.0000
K2P	36	-1882.0111	3836.0222	0.0000	1.0000
F81	38	-1882.5832	3841.1664	0.0000	1.0000
JC69G	36	-1891.3162	3854.6323	0.0000	1.0000
JC69IG	37	-1890.3350	3854.6701	0.0000	1.0000
JC69I	36	-1891.8528	3855.7056	0.0000	1.0000
JC69	35	-1913.9053	3897.8107	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1822.7653	3910.4401	0.4936	0.4936
HKYI	40	-1822.8349	3910.5792	0.4605	0.9541
HKYIG	41	-1821.8422	3915.2166	0.0453	0.9994
GTRG	44	-1816.8523	3925.1051	0.0003	0.9997
GTRI	44	-1817.2445	3925.8895	0.0002	1.0000
GTRIG	45	-1815.6999	3929.4229	0.0000	1.0000
HKY	39	-1847.0410	3952.3687	0.0000	1.0000
K2PG	37	-1858.3339	3961.7091	0.0000	1.0000
K2PI	37	-1858.6600	3962.3612	0.0000	1.0000
K2PIG	38	-1857.5944	3966.8529	0.0000	1.0000
GTR	43	-1842.7381	3970.2538	0.0000	1.0000
SYMG	41	-1849.7151	3970.9624	0.0000	1.0000
SYMI	41	-1850.2380	3972.0082	0.0000	1.0000
SYMIG	42	-1848.6664	3975.4877	0.0000	1.0000
F81G	39	-1859.9172	3978.1212	0.0000	1.0000
F81I	39	-1860.2423	3978.7714	0.0000	1.0000
F81IG	40	-1858.7422	3982.3939	0.0000	1.0000
K2P	36	-1882.0111	4002.4407	0.0000	1.0000
SYM	40	-1874.5306	4013.9707	0.0000	1.0000
F81	38	-1882.5832	4016.8304	0.0000	1.0000
JC69G	36	-1891.3162	4021.0508	0.0000	1.0000
JC69I	36	-1891.8528	4022.1241	0.0000	1.0000
JC69IG	37	-1890.3350	4025.7113	0.0000	1.0000
JC69	35	-1913.9053	4059.6065	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32246.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32246.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32246.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32246.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr1_32246.phylip = 1 - 752;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32246.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;


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

