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.
First, install the following dependencies:
Then install the Attotree Python package:
$ 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 outputPlease use Github issues.
See Releases.
