The Automatic Phylogenetic Tree Builder

The Automatic Phylogenetic (AutoPhylo) is used to generate phylogenetic trees automatically by sampling the selected database (e.g., NCBI nr) and performs all tasks associated with traditional phylogenetic tree building which includes trimming, dropping overly similar sequences, and generating an maximum likelihood (ML) tree using RAxML.

The user provides one protein sequence or multiple sequences and blast databases are used to sample sequences from phyla selected by the user e.g., The following can be used for phyla found in the human gut i.e., Actinobacteriota, Bacteroidota, Desulfobacterota, Firmicutes, Proteobacteria, Synergistota, Verrucomicrobiota, Fusobacteria.

Installation

The tool requires Python >= 3.11 and conda >= 4.12.0. The latest release can be installed directly from pip or this repository.

pip install autophylo

Or

Create a conda environment using the environment.yml file which installs all the dependencies (listed below).

conda env create -f environment.yml

Usage

conda activate autophylo

Install autophylo using tarball

Install the autophylo application within the created autophylo conda environment using a tarball.

python3 -m pip install /path/to/autophylo-1.0.0.tar.gz

Dependencies

The following are required dependencies (listed below):

• NCBI BLAST 2.15.0
• BLAST databases (version 5)
• FastTree 2.1.11
• MUSCLE 5.1.0
• RAxML 8.2.13
• GBLOCKS 0.91b
• USEARCH 12.0_beta
• seqkit 2.8.2
• Trimal 1.5.0
• biopython 1.84
• joblib 1.4.2

Download pre-formatted blast databases

(https://ftp.ncbi.nlm.nih.gov/blast/db/v5/README)

• The pre-formatted databases offer the following advantages:
  • Pre-formatting removes the need to run makeblastdb;
  • Species-level taxonomy ids are included for each database entry;
  • Databases are broken into smaller-sized volumes and are therefore easier to download;
  • Sequences in FASTA format can be generated from the pre-formatted databases by using the blastdbcmd utility;
  • A convenient script (update_blastdb.pl) is available in the blast+ package to download the pre-formatted databases.

download nr

update_blastdb.pl --source ncbi --decompress --blastdb_version 5  --verbose 2 --num_threads 30 nr > log.nr 2>&1

Update config file

Obtain path to dependencies programs using the $CONDA_PREFIX variable.

After activating the autophylo run the following command to get the path and use it to update the config file

(autophylo) echo $CONDA_PREFIX

Example config file

(autophylo) amos@Amogelangs-MacBook-Pro autophylo % echo $CONDA_PREFIX
/Users/amos/miniconda3/envs/autophylo

Updated config file

NOTE: The databases can be place anywhere in the filesystem and in this example they are in /Users/amos/datalake.

[DEFAULT]
ServerAliveInterval = 45
Compression = yes
CompressionLevel = 9
ForwardX11 = yes

[ALIGNMENT]
MUSCLE=/Users/amos/miniconda3/envs/autophylo/bin/muscle
TRIMAL=/Users/amos/miniconda3/envs/autophylo/bin/trimal

[TREE]
FastTree=/Users/amos/miniconda3/envs/autophylo/bin/FastTree
RAxML_PTHREADS=/Users/amos/miniconda3/envs/autophylo/bin/raxmlHPC-PTHREADS-AVX
RAxML_HYBRID=/Users/amos/miniconda3/envs/autophylo/bin/raxmlHPC-HYBRID-AVX

[CLUSTERING]
GBLOCKS=/Users/amos/miniconda3/envs/autophylo/bin/Gblocks
USEARCH=/Users/amos/miniconda3/envs/autophylo/bin/usearch

[DATABASES]
BLASTDB=/Users/amos/datalake/BLASTDB/NR/nr
TAXIDS=/Users/amos/datalake/BLASTDB/NR/taxids