Stijn Wittouck
Stijn Wittouck
Dear Zhemin, Thank you for making PEPPA publicly available and for putting the publication on bioRxiv, it's a very nice read! I managed to install PEPPA successfully and tried to...
Dear Xiao, Thank you for making SwiftOrtho available on GitHub! I tried to run the example and it passed test 1, but during test 2 there was an error; see...
Make a "quick start" section in the main README file and move demonstrations of more complicated analyses to a GitHub wiki. Example of a more complicated analysis to explain in...
It would be nice if the sample module was able to sample genomes within species (or genome groups in general), given a table with species assignments of genomes, similar to...
The hierarchical version of the pan module currently gathers orthogroups of pseudogenomes twice: once in phase 2 (pseudogenome creation), without storing the actual pseudogenome sequences, and once in phase 3...
The build module creates a profile database that consists of multiple sequence alignments (.aln files) and a list of score cutoffs for these alignments. The alignments are currently stored in...
Right now, orthogroup-specific hmmer score cutoffs are trained by taking the mean between the mean score of the positive examples and the mean score of the negative examples. However, it...