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author itaxotools
date Sun, 29 Jan 2023 16:25:48 +0000
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4e8e2f836d0f planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
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1 <h4>########################## PARAMETERS ######################</h4>
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2 <p> input file: test-data/Pontohedyle_COI.fas </p>
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3 <p> Coding gaps as characters: False </p>
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4 <p> Maximum undetermined nucleotides allowed: 5 </p>
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5 <p> Length of the alignment: 655 -> 655 </p>
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6 <p> Indexing reference: Not set </p>
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7 <p> Read in 27 sequences </p>
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8 <p> query taxa: 2 - brasilensis, joni </p>
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9 <p> Cutoff set as: 100 </p>
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10 <p> Number iterations of MolD set as: 10000 </p>
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11 <p> Maximum length of raw mDNCs set as: 12 </p>
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12 <p> Maximum length of refined mDNCs set as: 7 </p>
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13 <p> simulated sequences up to 1 percent divergent from original ones </p>
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14 <p> Maximum number of sequences modified per clade 10 </p>
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15 <p> scoring of the rDNCs; threshold in two consequtive runs: 75 </p>
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16 <h4>########################### RESULTS ##########################</h4>
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17 <h4>************** brasilensis **************</h4>
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18 <p> Sequences analyzed: 4 </p>
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19 <p> single nucleotide mDNCs*: 45 - 4: 'G', 16: 'C', 40: 'C', 44: 'G', 46: 'G', 68: 'G', 97: 'C', 101: 'C', 102: 'C', 167: 'G', 169: 'C', 170: 'T', 197: 'A', 202: 'G', 217: 'A', 227: 'G', 228: 'C', 239: 'T', 272: 'G', 287: 'A', 295: 'G', 310: 'C', 332: 'T', 357: 'A', 358: 'G', 365: 'T', 372: 'T', 387: 'C', 434: 'G', 456: 'G', 457: 'G', 467: 'G', 482: 'T', 483: 'G', 497: 'C', 499: 'T', 512: 'T', 518: 'A', 529: 'A', 535: 'G', 542: 'T', 543: 'C', 566: 'C', 619: 'G', 635: 'G' </p>
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20 <p> mDNCs* retrieved: 1048; Sites involved: 100; Independent mDNCs**: 71 </p>
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21 <p> Shortest retrieved mDNC*: [4: 'G'] </p>
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22 <p> 1 rDNC_score (100): [4] - 52 </p>
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23 <p> 2 rDNC_score (100): [4, 16] - 86 </p>
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24 <p> 3 rDNC_score (100): [4, 16, 40] - 93 </p>
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25 <p> Final rDNC***: [4: 'G', 16: 'C', 40: 'C'] </p>
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26 <p> The DNA diagnosis for the taxon brasilensis is: 'G' in the site 4, 'C' in the site 16, 'C' in the site 40. </p>
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27 <h4>************** joni **************</h4>
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28 <p> Sequences analyzed: 3 </p>
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29 <p> single nucleotide mDNCs*: 10 - 31: 'A', 85: 'G', 160: 'G', 283: 'G', 298: 'G', 451: 'G', 523: 'C', 526: 'A', 578: 'C', 580: 'T' </p>
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30 <p> mDNCs* retrieved: 2662; Sites involved: 100; Independent mDNCs**: 50 </p>
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31 <p> Shortest retrieved mDNC*: [31: 'A'] </p>
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32 <p> 1 rDNC_score (100): [31] - 65 </p>
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33 <p> 2 rDNC_score (100): [31, 85] - 97 </p>
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34 <p> 3 rDNC_score (100): [31, 85, 160] - 99 </p>
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35 <p> Final rDNC***: [31: 'A', 85: 'G', 160: 'G'] </p>
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36 <p> The DNA diagnosis for the taxon joni is: 'A' in the site 31, 'G' in the site 85, 'G' in the site 160. </p>
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37 <h4> ################################# EXPLANATIONS #################################### </h4>
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38 <p> * mDNC -(=minimal Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment, </p>
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39 <p> unique for a query taxon. Therefore it is sufficient to differentiate a query taxon from all reference taxa in a dataset. </p>
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40 <p> Because it comprises minimal necessary number of nucleotide sites to differentiate a query, any mutation in the mDNC in</p>
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41 <p> single specimen of a query taxon will automatically disqualify it as a diagnostic combination. </p>
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42 <p> </p>
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43 <p> ** two or more mDNCs are INDEPENDENT if they constitute non-overlapping sets of nucleotide sites. </p>
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44 <p> </p>
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45 <p> *** rDNC -(=robust/redundant Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment, </p>
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46 <p> unique for a query taxon and (likewise mDNC) sufficient to differentiate a query taxon from all reference taxa in a dataset. </p>
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47 <p> However, rDNC comprises more than a minimal necessary number of diagnostic sites, and therefore is robust to single nucleotide </p>
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48 <p> replacements. Even if a mutation arises in one of the rDNC sites, the remaining ones will (with high probability) remain sufficient </p>
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49 <p> to diagnose the query taxon </p>
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50 <h4> Final diagnosis corresponds to rDNC </h4>