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ma-compbio / Phylo-HMRF

MIT License
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random : input of edges and branch length as newick? #4

Open WandrilleD opened 4 years ago

WandrilleD commented 4 years ago

Hi, I know this is a bit random, but I stumbled here when a colleague asked me for help to understand your input format. I was able to help him, however, I was thinking that your edges.txt and branch.txt could advangeously be replaced by a single tree in newick format, which is the accepted standard way of representing simple binary trees with branch lengths in the phylogenetic community.

Perhaps there are technical/model-based llimitations that would prevent this?

Anyhow, I just wished to try to help you improve on your software which seems, otherwise, quite useful.

cheers.

yangymargaret commented 4 years ago

Hi WandrilleD @WandrilleD, Thank you very much for your suggestion. This is very helpful. We'll update the software by using the newick format to represent the tree structure and the branch lengths. Thanks!