
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:37 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_22059.phylip" (19 taxa, 558 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	-2308.7115	4703.7674	0.9995	0.9995
HKYIG	41	-2316.0107	4720.6957	0.0002	0.9997
GTRG	44	-2312.6583	4721.0359	0.0002	0.9999
GTRIG	45	-2312.6584	4723.4028	0.0001	1.0000
HKYI	40	-2319.3949	4725.1341	0.0000	1.0000
GTRI	44	-2316.4549	4728.6291	0.0000	1.0000
K2PG	37	-2328.3852	4736.1781	0.0000	1.0000
K2PIG	38	-2328.3852	4738.4814	0.0000	1.0000
K2PI	37	-2331.3373	4742.0822	0.0000	1.0000
SYMG	41	-2327.2666	4743.2076	0.0000	1.0000
SYMIG	42	-2327.2666	4745.5469	0.0000	1.0000
SYMI	41	-2330.3376	4749.3496	0.0000	1.0000
HKY	39	-2334.3991	4752.8214	0.0000	1.0000
GTR	43	-2330.9415	4755.2449	0.0000	1.0000
K2P	36	-2347.3665	4771.8463	0.0000	1.0000
SYM	40	-2345.7935	4777.9312	0.0000	1.0000
F81G	39	-2386.1165	4856.2561	0.0000	1.0000
F81IG	40	-2386.1164	4858.5772	0.0000	1.0000
F81I	39	-2388.8918	4861.8068	0.0000	1.0000
JC69G	36	-2400.5828	4878.2789	0.0000	1.0000
JC69IG	37	-2400.5829	4880.5734	0.0000	1.0000
JC69I	36	-2403.2020	4883.5172	0.0000	1.0000
F81	38	-2402.6874	4887.0858	0.0000	1.0000
JC69	35	-2417.4179	4909.6633	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2308.7115	4697.4231	0.9992	0.9992
GTRG	44	-2312.6583	4713.3166	0.0004	0.9996
HKYIG	41	-2316.0107	4714.0213	0.0002	0.9998
GTRIG	45	-2312.6584	4715.3168	0.0001	1.0000
HKYI	40	-2319.3949	4718.7898	0.0000	1.0000
GTRI	44	-2316.4549	4720.9098	0.0000	1.0000
K2PG	37	-2328.3852	4730.7704	0.0000	1.0000
K2PIG	38	-2328.3852	4732.7704	0.0000	1.0000
SYMG	41	-2327.2666	4736.5332	0.0000	1.0000
K2PI	37	-2331.3373	4736.6745	0.0000	1.0000
SYMIG	42	-2327.2666	4738.5333	0.0000	1.0000
SYMI	41	-2330.3376	4742.6751	0.0000	1.0000
HKY	39	-2334.3991	4746.7982	0.0000	1.0000
GTR	43	-2330.9415	4747.8830	0.0000	1.0000
K2P	36	-2347.3665	4766.7331	0.0000	1.0000
SYM	40	-2345.7935	4771.5869	0.0000	1.0000
F81G	39	-2386.1165	4850.2330	0.0000	1.0000
F81IG	40	-2386.1164	4852.2329	0.0000	1.0000
F81I	39	-2388.8918	4855.7837	0.0000	1.0000
JC69G	36	-2400.5828	4873.1656	0.0000	1.0000
JC69IG	37	-2400.5829	4875.1657	0.0000	1.0000
JC69I	36	-2403.2020	4878.4039	0.0000	1.0000
F81	38	-2402.6874	4881.3748	0.0000	1.0000
JC69	35	-2417.4179	4904.8358	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2308.7115	4870.3974	0.9999	0.9999
K2PG	37	-2328.3852	4890.7717	0.0000	0.9999
HKYIG	41	-2316.0107	4891.3200	0.0000	1.0000
HKYI	40	-2319.3949	4891.7642	0.0000	1.0000
K2PI	37	-2331.3373	4896.6758	0.0000	1.0000
K2PIG	38	-2328.3852	4897.0961	0.0000	1.0000
GTRG	44	-2312.6583	4903.5884	0.0000	1.0000
GTRIG	45	-2312.6584	4909.9130	0.0000	1.0000
GTRI	44	-2316.4549	4911.1816	0.0000	1.0000
SYMG	41	-2327.2666	4913.8319	0.0000	1.0000
HKY	39	-2334.3991	4915.4482	0.0000	1.0000
SYMI	41	-2330.3376	4919.9739	0.0000	1.0000
SYMIG	42	-2327.2666	4920.1564	0.0000	1.0000
K2P	36	-2347.3665	4922.4100	0.0000	1.0000
GTR	43	-2330.9415	4933.8305	0.0000	1.0000
SYM	40	-2345.7935	4944.5613	0.0000	1.0000
F81G	39	-2386.1165	5018.8830	0.0000	1.0000
F81I	39	-2388.8918	5024.4337	0.0000	1.0000
F81IG	40	-2386.1164	5025.2073	0.0000	1.0000
JC69G	36	-2400.5828	5028.8425	0.0000	1.0000
JC69I	36	-2403.2020	5034.0809	0.0000	1.0000
JC69IG	37	-2400.5829	5035.1670	0.0000	1.0000
F81	38	-2402.6874	5045.7004	0.0000	1.0000
JC69	35	-2417.4179	5056.1883	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/chr2_22059.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22059.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/chr2_22059.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22059.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/chr2_22059.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22059.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

