Concatenated maximum likelihood phylogeny inferred using RAxML, from the full 29 species, 107 locus dataset, converted to amino acid sequences, under the Dayhoff substitution model.
Part 1 of the web appendix describes the methods used to recover the original SDHS dataset; convert these data into a useable format; and identify, confirm, and verify the recovered data.
It can be a time-consuming operation on large datasets, converting in the order of 40 000 sequences per second, although this is only around 70% slower than converting SAM to BAM using SAMtools.
Fasta-formatted sequence files were aligned using MUSCLE, with aligned datasets converted to Nexus format using the program seqConverter.pl, version 1.1 [187].
As highly imbalanced problems, the satimage dataset and yeast dataset were converted into binary class problem: the class "damp grey soil" and the other classes in satimage, and the class "ME2" and the other classes in yeast.
To this end, eight molecular datasets (angiotensin converting enzyme, acetylcholinesterase inhibitors, benzodiazepine receptor, cyclooxygenase-2 inhibitors, dihydrofolate reductase inhibitors, glycogen phosphorylase b, thermolysin inhibitors, thrombin inhibitors) widely used as benchmarks in the evaluation of several procedures are utilized.
For large datasets, however, converting textual descriptions into a computer-readable format by human interaction is a tedious task.
Mutual information was calculated between each pair of datasets I D k; D i) using the discretization described above and, for each dataset pair, converted to a fraction by dividing by the total amount of possible shared information, I'(D k; D i) = I D k; D i /min(H(D k), H D i)).
The registered Drosophila first instar larval brain dataset was converted into a CATMAID compatible scale pyramid yielding 21 846 tiles per section and 1856910 tiles for the whole dataset.
We pre-process this dataset, and convert it into a specific XML format to mine it through the ProM (process mining) tool.
