FASTTREE
build phylogenetic trees using fasttree. Documentation found at http://www.microbesonline.org/fasttree/
Example
This wrapper can be used in the following way:
rule fasttree:
input:
alignment="{sample}.fa", # Input alignment file
output:
tree="{sample}.nwk", # Output tree file
log:
"logs/muscle/{sample}.log",
params:
extra="", # Additional arguments
wrapper:
"v5.8.0-3-g915ba34/bio/fasttree"
Note that input, output and log file paths can be chosen freely.
When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Notes
fasttree can only be run with a single thread.
Software dependencies
fasttree=2.1.11
Input/Output
Input:
Alignment FASTA or interleaved phylip file
Output:
Newick formatted tree file
Code
__author__ = "Nikos Tsardakas Renhuldt"
__copyright__ = "Copyright 2021, Nikos Tsardakas Renhuldt"
__email__ = "nikos.tsardakas_renhuldt@tbiokem.lth.se"
__license__ = "MIT"
from snakemake.shell import shell
import os
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
shell(
"fasttree "
"{extra} "
"{snakemake.input.alignment} "
"> {snakemake.output.tree} "
"{log}"
)