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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:

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>

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