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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
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How add phylogenetic tree in json file #149

Closed OrsonMM closed 4 years ago

OrsonMM commented 5 years ago

Dear team aliTV

Please I install and run alitv.pl and it only give me the cromosomes aligment. How can add the tree in my json file?

iimog commented 5 years ago

Hi @OrsonMM,

did you specify a tree file when you ran alitv.pl like described here: https://github.com/AliTVTeam/AliTV-perl-interface/blob/master/doc/alitv.md#section-tree

If so, which format did you use? Do the names in the tree file match your genome identifiers?

An important point to note is that AliTV does not calculate a phylogenetic tree. It is only capable of showing the tree alongside the alignment if it was provided by the user.

Happy to help you debug any issues you might face.

iimog commented 4 years ago

I assume this issue is fixed. Feel free to re-open if it is not.