treesapp 0.6.8

TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.

TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler

Overview

TreeSAPP is a python package for phylogenetically annotating proteins from genomes and metagenomes.

Quick start

We recommend installing TreeSAPP into it's own conda environment with the following command:

conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp
conda activate treesapp_cenv

For more options please visit the wiki page on Installing TreeSAPP.

To list all the sub-commands run treesapp.

To test the assign workflow, run:

treesapp assign -i TreeSAPP/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t M0701,M0702,M0705

To classify sequences in your genome of interest:

treesapp assign -i my.fasta -o ~/path/to/output/directory/

Tutorials

If we do not yet have a reference package for a gene you are interested in, please try building a new reference package. Of course, if you run into any problems or would like to collaborate on building many reference packages don't hesitate to email us or create a new issue with an 'enhancement' label.

To determine whether the sequences used to build your new reference package are what you think they are, and whether it might unexpectedly annotate homologous sequences, see the purity tutorial.

If you are working with a particularly complex reference package, from an orthologous group for example, or have extra phylogenetic information you'd like to include in your classifications, try annotating extra features with treesapp layer.

Yet to come

• Interpreting treesapp assign results
• Evaluating classification accuracy
• Taxonomically decorating trees for iTOL
• Terraform

Authors

• Connor Morgan-Lang (cmorganl, maintainer)
• Ryan McLaughlin (McGlock)
• Grace Zhang (grace72)
• Kevin Chan (kevinxchan)
• Zachary Armstrong
• Steven J. Hallam