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sestaton / tephra

A tool for discovering transposable elements and describing patterns of genome evolution
MIT License
30 stars 3 forks source link

LTR-RT feature clustering needs optimizing #13

Closed sestaton closed 8 years ago

sestaton commented 8 years ago

For some domains, such as the LTRs, the feature clustering for family classification is taking way too long to be practical. Need to consider alternatives or optimize the conditions with Vmatch.

sestaton commented 8 years ago

Fixed in v0.03.0. New indexing and sequence parsing methods that use HTSlib, as well as a new GFF3 feature parsing method that is much faster that the previous methods.