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

SNPs alignment as input #110

Open mlarjim opened 5 months ago

mlarjim commented 5 months ago

I have been using a core genome alignment as input of grapeTree stand-alone version, but it crashes when the alignment contains too many sequences because of a memory issue (I do not have enough memory resources in my computer).

So I was thinking about using a SNPs alignment (an alignment that just contains the nucleotides that have changed in any of the sequences), which is lighter than the cg alignment and less memory consuming. The resulting grapetree is slightly different Would that be a good approach for overcoming my memory issue?

Thank you in advance, Maria

lskatz commented 4 months ago

I coincidentally just wrote this up! Hope it's helpful. https://github.com/lskatz/lyve-SET/blob/master/docs/TIPS.md#a-word-on-grapetree-and-other-minimum-spanning-tree-software

mlarjim commented 4 months ago

Hi Lee, thank you for your comment. It does not solve my issue, but maybe I should meditate on using a minimum spanning tree to visualize an alignment. Depending on the species, organisms never share similar snps, so they will not be grouped together