phyca is built around Compleasm utilizing the NCBI Genome database. For a query assembly, phyca improves the precision of BUSCO/Compleasm annotations by up to 7%, makes syntenic comparisons to public reference genomes and rapidly places the assembly on a broad, precomputed phylogeny.
pip install phyca
phyca is distributed through PyPI and github. A working installation of Compleasm (including SEPP and pplacer) is necessary to avail all functionality. I recommend creating a conda environment to install Compleasm first and installing phyca in that environment, e.g.,
# create environment
conda create -n phyca python=3.9.19
# install compleasm
conda install bioconda::compleasm=0.2.6
# install phyca
pip install phyca
Note that as of 02/03/2025, there is a known issue with pplacer and SEPP on Debian-based systems. A working solution is provided here.
phyca has the following nonexhaustive dependency structure.
Python (tested with 3.9.19)
↓
│───numpy (tested with 2.0.2)
│───pandas (tested with 2.2.3)
│───matplotlib (tested with 3.9.4)
│───seaborn (tested with 0.13.2)
│───SciPy (tested with 1.13.1)
│───BioNick (tested with 0.0.7)
└───Compleasm (tested with 0.2.6)
│─── hmmer (tested with 3.1b2)
│─── miniprot (tested with 0.13-r248)
│ └─── libgcc (tested with 14.2.0 under conda)
└─── SEPP (tested with 4.4.0)
└─── pplacer and guppy (v1.1.alpha19-0-g807f6f3)
phyca supports 10 BUSCO lineages: viridiplantae, liliopsida, eudicots, chlorophyta, fungi, ascomycota, basidiomycota, metazoa, arthropoda and vertebrata.
A simple run on a query assembly, would be:
phyca -a <assembly_file> -l <lineage>
The Compleasm output folder can also be used as input if compleasm output was previously generated:
phyca -c <compleasm_direcoty> -l <lineage>
The above run will output BUSCO, CUSCO (Curated USCOs with higher precision) and MUSCO (remaining USCOs) statistics and graphs. It will compare the query to chromosome level genome assemblies from NCBI genome and output a table with a measure of synteny against each genome. It will output a Neighbor-Joining tree based on BUSCO synteny. Finally, it will place the assembly on a large precomputed phylogeny for the lineage and graph the observed decay in BUSCO synteny against inferred phylogenetic distance.
phyca allows syntenic comparisons between assemblies with compleasm annotations or any set of gene annotations formatted in the same way.
to compute the syntenic distance between two assemblies with the -s flag.
phyca -l <lineage> -s -a <assembly1> -r <assembly2>
The same comparison can be done by pointing to the compleasm output directoreis, if already available.
phyca -l <lineage> -s -c <assembly1_compdir> -m <assembly2_compdir>
Comparisons are done in the following way, adjust for variable query contiguity, and will produce the best results when one of the assemblies is highly contiguous and accurate:
The bulk data used by phyca is hosted by AGI's AVA cluster. All alignments, precomputed trees, annotations, metadata and more information is available at phyca.org.
USCO graph:
Synteny decay plot:
Placement tree snippet:
