A tool for generating cladograms and analyzing sequences from pangenomes.
Tightly coupled with data from COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource (for now).
The kind of cladogram that taxophages can generate is here: an rsvd tree for ~25k sequences.
Refer to the docs directory.
$ python main.py -h
Usage: main.py [OPTIONS] COMMAND [ARGS]...
Taxophages: coverage matrix analysis and phylogenetics
Options:
-h, --help Show this message and exit
Commands:
clado-rsvd Combines cladogram and rsvd
cladogram Compute pairwise distances and generate a cladogram
count Count number of bases & Ns in a fasta file
extract-field Pull out a single field into a txt file
filter-csv Filter the coverage vector using ids in txt file
fun Pointless fun
metadata Specific to the COViD dataset
qc Filter sequences for Ns below given threshold
rsvd Perform rsvd on a coverage matrix
sample Take a random sample from a coverage matrix