Hello,
is there any user-friendly, publicly available resource to generate a phylogenetic tree from an ANI distance matrix?
Thanks a lot,
Ralf
Hi Ralf
I do not know what is ANI but MEGA can buid a tree from any ditance matrix
Cheers
Thierry
Thanks a lot, Thierry,
I will look into this. ANI = Average Nucleotide Identity (at a genome-wide scale).
Best, Ralf
Dear Dr. Ralf,
You can use GENE-E (https://software.broadinstitute.org/GENE-E/). Its a java based web tool.
Best,
Vasvi
Thanks a lot, Vasvi,
I will have a look after the holidays.
All the best for 2017!
Ralf
Hello Ralf, happy 2017!
I've been working on this resource that you may find useful: http://enve-omics.ce.gatech.edu/g-matrix, as part of the enveomics collection.
It's very recent and still in beta-testing, but you're welcome to use it. It builds an ANI (or AAI) matrix from a collection of input genomes (or proteomes) and constructs a clustering from this matrix. Note that this may not be a phylogenetic tree, since no evolutionary model is assumed. However, we've seen a good correlation of these ANI trees with phylogenetic trees, and are much more tractable (computationally) than full phylogenomic reconstructions.
Best, Miguel.
http://enve-omics.ce.gatech.edu/g-matrix
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