<div dir="ltr">Dear MAKER-devel group<div><br></div><div>I have been testing out MAKER3 beta version and found out that EVM always returns much less number of models. Did any one experience this before? I do expect that EVM will return less models when compare to other, but not to this extend (only 20% of the expected gene models). Any suggestion would be much appreciated.</div><div><br></div><div>## Number of models obtained by each gene predictors:</div><div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(213,59,211)"><span style="font-variant-ligatures:no-common-ligatures">HLIG.all.maker.augustus_masked.proteins.fasta</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">11224</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(213,59,211)"><span style="font-variant-ligatures:no-common-ligatures">HLIG.all.maker.evm.proteins.fasta</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">1974</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(213,59,211)"><span style="font-variant-ligatures:no-common-ligatures">HLIG.all.maker.genemark.proteins.fasta</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">11352</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(213,59,211)"><span style="font-variant-ligatures:no-common-ligatures">HLIG.all.maker.proteins.fasta</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">13672</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(213,59,211)"><span style="font-variant-ligatures:no-common-ligatures">HLIG.all.maker.snap_masked.proteins.fasta</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(51,187,200)">:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)">13404</span></p></div><div><br></div><div>## maker_evm.ctl</div><div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">#-----Transcript weights</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmtrans=10 #default weight for source unspecified est/alt_est alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmtrans:blastn=0 #weight for blastn sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmtrans:est2genome=10 #weight for est2genome sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmtrans:tblastx=0 #weight for tblastx sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmtrans:cdna2genome=7 #weight for cdna2genome sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">#-----Protein weights</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmprot=10 #default weight for source unspecified protein alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmprot:blastx=2 #weight for blastx sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmprot:protein2genome=10 #weight for protein2genome sourced alignments</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">#-----Abinitio Prediction weights</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmab=10 #default weight for source unspecified ab initio predictions</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmab:snap=7 #weight for snap sourced predictions</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmab:augustus=10 #weight for augustus sourced predictions</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmab:fgenesh=10 #weight for fgenesh sourced predictions</span></p>
<p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">evmab:genemark=10 #weight for genemark sourced predictions</span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Regards,</p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Tuan</p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p></div></div>