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planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
| author | itaxotools |
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| date | Sun, 29 Jan 2023 16:25:48 +0000 |
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| -1:000000000000 | 0:4e8e2f836d0f |
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| 1 <h4>########################## PARAMETERS ######################</h4> | |
| 2 <p> input file: test-data/Pontohedyle_COI.fas </p> | |
| 3 <p> Coding gaps as characters: False </p> | |
| 4 <p> Maximum undetermined nucleotides allowed: 5 </p> | |
| 5 <p> Length of the alignment: 655 -> 655 </p> | |
| 6 <p> Indexing reference: Not set </p> | |
| 7 <p> Read in 27 sequences </p> | |
| 8 <p> query taxa: 2 - brasilensis, joni </p> | |
| 9 <p> Cutoff set as: 100 </p> | |
| 10 <p> Number iterations of MolD set as: 10000 </p> | |
| 11 <p> Maximum length of raw mDNCs set as: 12 </p> | |
| 12 <p> Maximum length of refined mDNCs set as: 7 </p> | |
| 13 <p> simulated sequences up to 1 percent divergent from original ones </p> | |
| 14 <p> Maximum number of sequences modified per clade 10 </p> | |
| 15 <p> scoring of the rDNCs; threshold in two consequtive runs: 75 </p> | |
| 16 <h4>########################### RESULTS ##########################</h4> | |
| 17 <h4>************** brasilensis **************</h4> | |
| 18 <p> Sequences analyzed: 4 </p> | |
| 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> | |
| 20 <p> mDNCs* retrieved: 1048; Sites involved: 100; Independent mDNCs**: 71 </p> | |
| 21 <p> Shortest retrieved mDNC*: [4: 'G'] </p> | |
| 22 <p> 1 rDNC_score (100): [4] - 52 </p> | |
| 23 <p> 2 rDNC_score (100): [4, 16] - 86 </p> | |
| 24 <p> 3 rDNC_score (100): [4, 16, 40] - 93 </p> | |
| 25 <p> Final rDNC***: [4: 'G', 16: 'C', 40: 'C'] </p> | |
| 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> | |
| 27 <h4>************** joni **************</h4> | |
| 28 <p> Sequences analyzed: 3 </p> | |
| 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> | |
| 30 <p> mDNCs* retrieved: 2662; Sites involved: 100; Independent mDNCs**: 50 </p> | |
| 31 <p> Shortest retrieved mDNC*: [31: 'A'] </p> | |
| 32 <p> 1 rDNC_score (100): [31] - 65 </p> | |
| 33 <p> 2 rDNC_score (100): [31, 85] - 97 </p> | |
| 34 <p> 3 rDNC_score (100): [31, 85, 160] - 99 </p> | |
| 35 <p> Final rDNC***: [31: 'A', 85: 'G', 160: 'G'] </p> | |
| 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> | |
| 37 <h4> ################################# EXPLANATIONS #################################### </h4> | |
| 38 <p> * mDNC -(=minimal Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment, </p> | |
| 39 <p> unique for a query taxon. Therefore it is sufficient to differentiate a query taxon from all reference taxa in a dataset. </p> | |
| 40 <p> Because it comprises minimal necessary number of nucleotide sites to differentiate a query, any mutation in the mDNC in</p> | |
| 41 <p> single specimen of a query taxon will automatically disqualify it as a diagnostic combination. </p> | |
| 42 <p> </p> | |
| 43 <p> ** two or more mDNCs are INDEPENDENT if they constitute non-overlapping sets of nucleotide sites. </p> | |
| 44 <p> </p> | |
| 45 <p> *** rDNC -(=robust/redundant Diagnostic nucleotide combination) is a combination of nucleotides at specified sites of the alignment, </p> | |
| 46 <p> unique for a query taxon and (likewise mDNC) sufficient to differentiate a query taxon from all reference taxa in a dataset. </p> | |
| 47 <p> However, rDNC comprises more than a minimal necessary number of diagnostic sites, and therefore is robust to single nucleotide </p> | |
| 48 <p> replacements. Even if a mutation arises in one of the rDNC sites, the remaining ones will (with high probability) remain sufficient </p> | |
| 49 <p> to diagnose the query taxon </p> | |
| 50 <h4> Final diagnosis corresponds to rDNC </h4> |