search

achtman-lab / GrapeTree

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
https://genome.cshlp.org/content/28/9/1395
GNU General Public License v3.0
79 stars 27 forks source link

How to make phylogenetic using binary data #103

Open sekhwal opened 2 years ago

sekhwal commented 2 years ago

I am trying to make phylogenetic tree using binary data. I tried using grapetree -p MGE_binary.txt -m MSTreeV2 >out.phy. Please suggest.

Example Input file:

         C1  C3  C5  D1

gene1 1 0 1 0 gene2 0 1 0 1 gene2 1 0 0 1 geen3 1 1 0 1

happykhan commented 2 years ago

Grapetree isnt really designed for this data. you can make a tree from binary data in something like IQTREE. http://www.iqtree.org/doc/Tutorial#binary-morphological-and-snp-data and then visualize the resulting tree file with grapetree.