SCARAP
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SWittouck
A toolkit for prokaryotic comparative genomics
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...
Closes #21 I also added a constants.py where I've put a few recurring strings I had encountered while making changes.
