Attotree

Introduction

Rapid estimation of phylogenetic trees directly from FASTA files in the style of Mashtree. With the default options, its output is identical to Mashtree, but the computation takes only a fraction of time.

Installation

Using Bioconda

conda install -y -c bioconda -c conda-forge attotree

Using PyPI

First, install the following dependencies:

• Mash
• QuickTree

Then install the Attotree Python package:

pip install -U attotree

Quick example

conda install attotree
attotree tests/*.fa

Command-line parameters

$ attotree -h

Program: attotree (rapid estimation of phylogenetic trees using sketching)
Version: 0.1.6
Author:  Karel Brinda <karel.brinda@inria.fr>

usage: attotree [-k INT] [-s INT] [-t INT] [-o FILE] [-m STR] [-d DIR] [-L] [-D] [-V] genome [genome ...]

positional arguments:
  genome      input genome file(s) (fasta / gzipped fasta / list of files when "-L")

options:
  -h          show this help message and exit
  -v          show program's version number and exit
  -k INT      kmer size [21]
  -s INT      sketch size [10000]
  -t INT      number of threads [#cores, 10]
  -o FILE     newick output [-]
  -m STR      tree construction method (nj/upgma) [nj]
  -d DIR      tmp dir [default system, /var/folders/z6...]
  -L          input files are list of files
  -D          debugging (don't remove tmp dir)
  -V          verbose output

Issues

Please use Github issues.

Changelog

See Releases.

Licence

MIT

Authors

Karel Brinda <karel.brinda@inria.fr>