Codeml BEB positive sites don't match amino acids in alignment
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21 months ago

I'm trying to look at potential positive selection sites in genes of interest using EasyCodeml. I can run the GUI, but the results don't always match my protein sequences. Does anyone know what causes this?

GUI OUTPUT: Branch site model (BSM)
Model np Ln L Estimates of parameters Model compared LRT P-value Positive sites Model A 16 -2510.225991 Site class 0 1 2a 2b Model A vs.Model A null 0.046986273 3 L 0.672,12 N 0.524,21 S 0.558,39 A 0.507,97 S 0.519,102 C 0.551,110 G 0.560,116 T 0.522,125 R 0.516,154 R 0.537,157 C 0.852,162 S 0.578,168 L 0.575,171 N 0.574,179 R 0.501,185 R 0.562 f 0.38068 0.52904 0.03778 0.05250
ω0 1.00000 1.00000 1.00000 1.00000
ω1 1.00000 1.00000 17.13576 17.13576
Model A null 15 -2512.198931 1 Not Allowed

AA SEQUENCE: MLQTVGPCGLRLLPPLPVLLLLASADREAGLPKATLSLDPPWVNVLQGDNVTLTCRGAPGPGSPATRWFHNGNFLETQAQSSYSLTANSSDSGNYTCHTAQTSLSDPVHLDVVSDWLLLQTPRLLFQEGEPIVLRCHSWKGWPLYKVTFFHNKTSRKFSHTDFIFSIPRANSSHSGKYHCTGFIRKSRYSSQAVSIAVRGPAVPSISPLFALWPQITFCLVMGLLFAVDTGLYFSMKRDLRRLMGDWTNGKVTWSKSPEDK

codeml positve selection branch-site model paml • 365 views
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