Collapse banches wirh low support

tjunier / newick_utils

shell tools for processing phylogenetic trees

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Collapse banches wirh low support #24

Open kmeusemann opened 4 years ago

kmeusemann commented 4 years ago

Hi, I read in several papers that with Newick Utils I can also collapse via command line lets say low supportet branches into polytomies. How can I do this ? (command line) Many thanks in advance!

estolle commented 4 years ago

should be: nw_ed genetrees.tre 'i & b<=10' o > genetrees.BS10.tre

" "open" all nodes with bootstrap support <= 10 (assuming support is coded in internal node labels)"

o / open --> " (splice Out) splice out node, and attach children to parent, preserving branch lengths. This is useful for "opening" poorly supported nodes"