
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:36 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_7243.phylip" (19 taxa, 268 characters)

Minimum AIC  model: GTRI
Minimum AICc model: K2PI
Minimum BIC  model: K2PI


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
K2PI	37	-581.3615	1248.9491	0.2240	0.2240
HKYI	40	-577.2563	1248.9620	0.2225	0.4465
HKYG	40	-577.7182	1249.8858	0.1402	0.5867
K2PG	37	-582.0230	1250.2720	0.1156	0.7022
GTRI	44	-572.8895	1251.5367	0.0614	0.7637
K2PIG	38	-581.3617	1251.6667	0.0575	0.8212
HKYIG	41	-577.2565	1251.7519	0.0551	0.8764
GTRG	44	-573.1408	1252.0394	0.0478	0.9241
SYMI	41	-577.7845	1252.8079	0.0325	0.9566
SYMG	41	-578.2414	1253.7217	0.0206	0.9772
GTRIG	45	-572.8811	1254.4108	0.0146	0.9918
SYMIG	42	-577.7848	1255.6230	0.0080	0.9998
HKY	39	-586.7221	1265.1285	0.0001	0.9999
K2P	36	-591.3304	1266.1932	0.0000	0.9999
GTR	43	-581.8036	1266.5000	0.0000	0.9999
JC69I	36	-592.3553	1268.2430	0.0000	0.9999
F81I	39	-588.3708	1268.4258	0.0000	1.0000
SYM	40	-587.1815	1268.8123	0.0000	1.0000
JC69G	36	-592.7277	1268.9879	0.0000	1.0000
F81G	39	-588.6998	1269.0837	0.0000	1.0000
JC69IG	37	-592.3554	1270.9369	0.0000	1.0000
F81IG	40	-588.3710	1271.1914	0.0000	1.0000
F81	38	-597.4276	1283.7984	0.0000	1.0000
JC69	35	-601.5621	1283.9864	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-572.8895	1233.7789	0.2344	0.2344
GTRG	44	-573.1408	1234.2816	0.1823	0.4167
HKYI	40	-577.2563	1234.5126	0.1624	0.5790
HKYG	40	-577.7182	1235.4364	0.1023	0.6814
GTRIG	45	-572.8811	1235.7622	0.0869	0.7683
HKYIG	41	-577.2565	1236.5130	0.0597	0.8280
K2PI	37	-581.3615	1236.7230	0.0538	0.8818
SYMI	41	-577.7845	1237.5690	0.0352	0.9170
K2PG	37	-582.0230	1238.0459	0.0278	0.9448
SYMG	41	-578.2414	1238.4827	0.0223	0.9671
K2PIG	38	-581.3617	1238.7235	0.0198	0.9869
SYMIG	42	-577.7848	1239.5696	0.0130	0.9998
GTR	43	-581.8036	1249.6071	0.0001	0.9999
HKY	39	-586.7221	1251.4443	0.0000	1.0000
SYM	40	-587.1815	1254.3630	0.0000	1.0000
K2P	36	-591.3304	1254.6607	0.0000	1.0000
F81I	39	-588.3708	1254.7415	0.0000	1.0000
F81G	39	-588.6998	1255.3995	0.0000	1.0000
JC69I	36	-592.3553	1256.7106	0.0000	1.0000
F81IG	40	-588.3710	1256.7421	0.0000	1.0000
JC69G	36	-592.7277	1257.4554	0.0000	1.0000
JC69IG	37	-592.3554	1258.7108	0.0000	1.0000
F81	38	-597.4276	1270.8551	0.0000	1.0000
JC69	35	-601.5621	1273.1243	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-581.3615	1369.5895	0.6240	0.6240
K2PG	37	-582.0230	1370.9124	0.3220	0.9460
K2PIG	38	-581.3617	1375.1810	0.0381	0.9841
HKYI	40	-577.2563	1378.1521	0.0086	0.9927
HKYG	40	-577.7182	1379.0759	0.0054	0.9981
HKYIG	41	-577.2565	1383.7434	0.0005	0.9987
K2P	36	-591.3304	1383.9363	0.0005	0.9991
SYMI	41	-577.7845	1384.7994	0.0003	0.9995
SYMG	41	-578.2414	1385.7132	0.0002	0.9996
JC69I	36	-592.3553	1385.9861	0.0002	0.9998
JC69G	36	-592.7277	1386.7310	0.0001	0.9999
SYMIG	42	-577.7848	1390.3911	0.0000	1.0000
HKY	39	-586.7221	1391.4928	0.0000	1.0000
JC69IG	37	-592.3554	1391.5774	0.0000	1.0000
GTRI	44	-572.8895	1391.7823	0.0000	1.0000
GTRG	44	-573.1408	1392.2850	0.0000	1.0000
F81I	39	-588.3708	1394.7900	0.0000	1.0000
F81G	39	-588.6998	1395.4480	0.0000	1.0000
GTRIG	45	-572.8811	1397.3566	0.0000	1.0000
SYM	40	-587.1815	1398.0025	0.0000	1.0000
JC69	35	-601.5621	1398.8088	0.0000	1.0000
F81IG	40	-588.3710	1400.3815	0.0000	1.0000
GTR	43	-581.8036	1404.0196	0.0000	1.0000
F81	38	-597.4276	1407.3126	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip = 1 - 268;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7243.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

