How to make phylogenetic using binary data

[sekhwal]

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]

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.