
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:59 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/chr3_3107.phylip" (19 taxa, 176 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: HKY


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	-545.3862	1195.0687	0.3321	0.3321
HKYI	40	-545.7130	1195.7222	0.2395	0.5717
HKY	39	-547.9228	1196.7867	0.1407	0.7123
GTRG	44	-539.5619	1197.3528	0.1060	0.8183
HKYIG	41	-545.3848	1198.4711	0.0606	0.8789
GTRI	44	-540.2360	1198.7010	0.0540	0.9330
GTR	43	-542.1047	1198.8760	0.0495	0.9824
GTRIG	45	-539.5664	1200.9789	0.0173	0.9997
K2PG	37	-558.3949	1211.1666	0.0001	0.9998
K2PI	37	-558.5307	1211.4381	0.0001	0.9999
K2P	36	-561.3798	1213.9250	0.0000	1.0000
K2PIG	38	-558.3796	1214.3942	0.0000	1.0000
SYMG	41	-554.7483	1217.1982	0.0000	1.0000
SYMI	41	-555.0279	1217.7573	0.0000	1.0000
SYM	40	-557.3571	1219.0105	0.0000	1.0000
F81G	39	-559.3034	1219.5481	0.0000	1.0000
F81I	39	-559.4987	1219.9385	0.0000	1.0000
SYMIG	42	-554.7400	1220.6380	0.0000	1.0000
F81	38	-562.1398	1221.9146	0.0000	1.0000
F81IG	40	-559.2962	1222.8887	0.0000	1.0000
JC69G	36	-571.7511	1234.6676	0.0000	1.0000
JC69I	36	-571.8524	1234.8704	0.0000	1.0000
JC69	35	-574.6192	1237.2385	0.0000	1.0000
JC69IG	37	-571.7364	1237.8496	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-539.5619	1167.1238	0.4063	0.4063
GTRI	44	-540.2360	1168.4720	0.2070	0.6133
GTRIG	45	-539.5664	1169.1327	0.1488	0.7621
GTR	43	-542.1047	1170.2094	0.0869	0.8489
HKYG	40	-545.3862	1170.7724	0.0655	0.9145
HKYI	40	-545.7130	1171.4259	0.0473	0.9617
HKYIG	41	-545.3848	1172.7696	0.0241	0.9859
HKY	39	-547.9228	1173.8455	0.0141	1.0000
K2PG	37	-558.3949	1190.7897	0.0000	1.0000
K2PI	37	-558.5307	1191.0613	0.0000	1.0000
SYMG	41	-554.7483	1191.4967	0.0000	1.0000
SYMI	41	-555.0279	1192.0558	0.0000	1.0000
K2PIG	38	-558.3796	1192.7591	0.0000	1.0000
SYMIG	42	-554.7400	1193.4801	0.0000	1.0000
SYM	40	-557.3571	1194.7142	0.0000	1.0000
K2P	36	-561.3798	1194.7596	0.0000	1.0000
F81G	39	-559.3034	1196.6069	0.0000	1.0000
F81I	39	-559.4987	1196.9974	0.0000	1.0000
F81IG	40	-559.2962	1198.5924	0.0000	1.0000
F81	38	-562.1398	1200.2795	0.0000	1.0000
JC69G	36	-571.7511	1215.5021	0.0000	1.0000
JC69I	36	-571.8524	1215.7049	0.0000	1.0000
JC69IG	37	-571.7364	1217.4728	0.0000	1.0000
JC69	35	-574.6192	1219.2385	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-547.9228	1297.4944	0.3634	0.3634
HKYG	40	-545.3862	1297.5918	0.3461	0.7095
HKYI	40	-545.7130	1298.2453	0.2497	0.9592
HKYIG	41	-545.3848	1302.7594	0.0261	0.9853
GTR	43	-542.1047	1306.5402	0.0039	0.9892
GTRG	44	-539.5619	1306.6251	0.0038	0.9930
GTRI	44	-540.2360	1307.9733	0.0019	0.9950
K2PG	37	-558.3949	1308.0976	0.0018	0.9968
K2PI	37	-558.5307	1308.3692	0.0016	0.9983
K2P	36	-561.3798	1308.8970	0.0012	0.9996
GTRIG	45	-539.5664	1311.8045	0.0003	0.9998
K2PIG	38	-558.3796	1313.2375	0.0001	1.0000
F81G	39	-559.3034	1320.2558	0.0000	1.0000
F81I	39	-559.4987	1320.6462	0.0000	1.0000
F81	38	-562.1398	1320.7579	0.0000	1.0000
SYMG	41	-554.7483	1321.4865	0.0000	1.0000
SYM	40	-557.3571	1321.5336	0.0000	1.0000
SYMI	41	-555.0279	1322.0456	0.0000	1.0000
F81IG	40	-559.2962	1325.4117	0.0000	1.0000
SYMIG	42	-554.7400	1326.6404	0.0000	1.0000
JC69G	36	-571.7511	1329.6396	0.0000	1.0000
JC69I	36	-571.8524	1329.8423	0.0000	1.0000
JC69	35	-574.6192	1330.2054	0.0000	1.0000
JC69IG	37	-571.7364	1334.7807	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/chr3_3107.phylip = 1 - 176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3107.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3107.phylip = 1 - 176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3107.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 (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3107.phylip = 1 - 176;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3107.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

