anvi-gen-phylogenomic-tree

Generate phylogenomic tree from aligment file.

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Authors

Özcan C. Esen
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A. Murat Eren (Meren)
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Requires

concatenated-gene-alignment-fasta

Provides

phylogeny

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.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-gen-phylogenomic-tree.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-gen-phylogenomic-tree [-h] -f FASTA file -o FILE_PATH [--program PROGRAM_NAME] [--just-do-it]

Parameters and their descriptions

INPUT FILES Concatenated aligment files exported using anvi-get-sequences-for-gene-clusters
-f, --fasta-file FASTA FILE required
A FASTA-formatted input file.
OUTPUT FILE The output file where the generated newick tree will be stored.
-o, --output-file FILE_PATH required
File path to store results.
PROGRAM The program that will be used for generating tree. Available options: default, fasttree
--program PROGRAM_NAME
Program name. Default: default
OTHERS Parameters of convenience
--just-do-it
Don't bother me with questions or warnings, just do it.

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.

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