anvi-gen-phylogenomic-tree
Table of Contents
Generate phylogenomic tree from aligment file.
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Authors
Can consume
concatenated-gene-alignment-fasta 
Can provide
Usage
This program generates a NEWICK-formatted phylogenomic tree (see phylogeny) based on a given concatenated-gene-alignment-fasta.
As mentioned in the phylogenetics tutorial, it currently only has the option to use FastTree to do so, but be aware that there are many other programs that you can do this with. Some of the options we are familiar with (and are not yet represented in anvi-gen-phylogenomic-tree) include MrBayes, MEGA, and PHYLIP, among many others, most of which will happily take a concatenated-gene-alignment-fasta.
Anyway, running this program is simple. Just provide the concatenated-gene-alignment-fasta with all of the genes that you want to use and the output file path for your phylogeny:
anvi-gen-phylogenomic-tree -f concatenated-gene-alignment-fasta \ -o PATH/TO/phylogeny
Edit this file to update this information.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.