description
Project description
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
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