This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.
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Improve documentation about automated phylogeny #52
If an automatic phylogenetic tree is produced via GToTree, it's possible that some low-quality genome sequences will be filtered out by GToTree during tree construction. These will then be removed from the final heatmap with a warning thrown to the user that they were removed.
We should consider better documenting this behaviour so that users are not confused by disappearing genomes. We could also make the warning more explicit.
No support for eukaryotic genomes
GToTree only works for prokaryotic genomes unless a custom HMM set for eukaryotes is included, which is outside of the design framework of this tool currently. We should either document this or build a way for eukaryotic genomes to be compatible.
jmtsuji
commented
4 years ago
Better reporting of removed genomes
If an automatic phylogenetic tree is produced via GToTree, it's possible that some low-quality genome sequences will be filtered out by GToTree during tree construction. These will then be removed from the final heatmap with a warning thrown to the user that they were removed.
We should consider better documenting this behaviour so that users are not confused by disappearing genomes. We could also make the warning more explicit.
No support for eukaryotic genomes
GToTree only works for prokaryotic genomes unless a custom HMM set for eukaryotes is included, which is outside of the design framework of this tool currently. We should either document this or build a way for eukaryotic genomes to be compatible.