Symptom: the selected_blast *.sel files contain numbers when they should contain sequence information. As far as I can tell, this problem will be more likely with genomic data than transcriptomic, but could effect either.

Diagnosis: During the extract_blast step, the regex/match is searching for a certain number of characters in to start extracting the sequence. It does not match in splitting on spaces, because if if the sequence position changes in number of digits, for example 999 to 1000, the space disappears and the regex splits on the wrong space. This is actually a little tricky to fix, but I know how to do it.

treecleaner works best with a single high hit being taken. some people might want to expand the range of

1. number of high hits taken
2. the width of high hit threshold. at the moment it is 3 order of magnitude from highest hit (unless it is 0.0, in which case all 0.0 hits are taken.)

Added a section to manual, but it isn't complete because treecleaner.pl hasn't had a full bugtest or warnings added.