Table 1 The four proposed workflow encoding schemes and their associated weight vectors for the five real-life bioinformatics workflows depicted in Figure 1
Encoding of type I | W1 | W2 | W3 | W4 | W5 | Weights for encoding of type I |
|---|---|---|---|---|---|---|
Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.35 |
ClustalW2 | 0 | 1 | 0 | 0 | 1 | 0.49 |
HGT Detector 3.2 | 1 | 1 | 1 | 0 | 1 | 0.88 |
Muscle | 1 | 0 | 0 | 0 | 1 | 0.41 |
PROTML (Phylip) | 1 | 0 | 0 | 0 | 0 | 0.68 |
PhyML (1) | 0 | 1 | 1 | 0 | 1 | 1.13 |
PhyML (2) | 0 | 0 | 0 | 0 | 1 | 1.13 |
Probcons | 0 | 0 | 1 | 0 | 0 | 0.55 |
Robinson & Foulds distance | 0 | 0 | 0 | 1 | 0 | 0.25 |
SEQBOOT | 1 | 0 | 0 | 0 | 0 | 0.14 |
Seq-Gen | 0 | 1 | 0 | 1 | 0 | 0.43 |
Encoding of type II | W1 | W2 | W3 | W4 | W5 | Weights for encoding of type II |
Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.10 |
ClustalW2 | 0 | 1 | 0 | 0 | 1 | 0.10 |
HGT Detector 3.2 | 1 | 1 | 1 | 0 | 1 | 1.00 |
Muscle | 1 | 0 | 0 | 0 | 1 | 0.10 |
PROTML (Phylip) | 1 | 0 | 0 | 0 | 0 | 0.10 |
PhyML | 0 | 1 | 1 | 0 | 2 | 0.10 |
Probcons | 0 | 0 | 1 | 0 | 0 | 0.10 |
Robinson&Foulds distance | 0 | 0 | 0 | 1 | 0 | 0.10 |
SEQBOOT | 1 | 0 | 0 | 0 | 0 | 0.10 |
Seq-Gen | 0 | 1 | 0 | 1 | 0 | 0.10 |
Encoding of type III | W1 | W2 | W3 | W4 | W5 | Weights for encoding of type III |
Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.35 |
HGT Detector 3.2 | 1 | 1 | 1 | 0 | 1 | 0.88 |
Robinson & Foulds distance | 0 | 0 | 0 | 1 | 0 | 0.25 |
ClustalW2 → PhyML | 0 | 1 | 0 | 0 | 1 | 1.62 |
Muscle → PhyML | 0 | 0 | 0 | 0 | 1 | 1.54 |
Muscle → SEQBOOT (Phylip) | 1 | 0 | 0 | 0 | 0 | 0.55 |
PROTML (Phylip) → HGT Detector 3.2 | `1 | 0 | 0 | 0 | 0 | 1.56 |
PhyML → HGT Detector 3.2 | 0 | 1 | 1 | 0 | 2 | 2.01 |
Probcons → PhyML | 0 | 0 | 1 | 1 | 0 | 1.68 |
SEQBOOT (Phylip) → PROTML (Phylip | 1 | 0 | 0 | 0 | 0 | 0.82 |
Seq-Gen → Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.78 |
Seq-Gen → ClustalW2 | 0 | 1 | 0 | 0 | 0 | 0.92 |
Encoding of type IV | W1 | W2 | W3 | W4 | W5 | Weights for encoding of type IV |
Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.10 |
HGT Detector 3.2 | 1 | 1 | 1 | 0 | 1 | 1.00 |
Robinson & Foulds distance | 0 | 0 | 0 | 1 | 0 | 0.10 |
ClustalW2 → PhyM | 0 | 1 | 0 | 0 | 1 | 0.10 |
Muscle → PhyML | 0 | 0 | 0 | 0 | 1 | 0.10 |
Muscle → SEQBOOT (Phylip) | 1 | 0 | 0 | 0 | 0 | 0.10 |
PROTML (Phylip) → HGT Detector 3.2 | 1 | 0 | 0 | 0 | 0 | 1.00 |
PhyML → HGT Detector 3.2 | 0 | 1 | 1 | 0 | 2 | 1.00 |
Probcons → PhyML | 0 | 0 | 1 | 0 | 0 | 0.10 |
SEQBOOT (Phylip) → PROTML (Phylip) | 1 | 0 | 0 | 0 | 0 | 0.10 |
Seq-Gen → Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 0.10 |
Seq-Gen → ClustalW2 | 0 | 1 | 0 | 0 | 0 | 0.10 |
INPUT_Sequences | 1 | 0 | 1 | 0 | 1 | 1.00 |
INPUT_Tree | 1 | 1 | 1 | 2 | 0 | 1.00 |
OUTPUT_Blast (NCBI) | 0 | 0 | 0 | 1 | 0 | 1.00 |
OUTPUT_Matrix | 1 | 1 | 1 | 1 | 1 | 1.00 |
OUTPUT_MultipleTrees | 0 | 0 | 0 | 1 | 0 | 1.00 |
OUTPUT_OutputText | 1 | 1 | 1 | 2 | 1 | 1.00 |
OUTPUT_Results | 1 | 1 | 1 | 1 | 1 | 1.00 |