Purdue University

Plink2 is a whole genome association analysis toolset.

Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.

Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing. Notably tools are included for generating and analyzing draft assemblies. Many of these tools are used by the research data analysis group at Oxford Nanopore Technologies.

PopPUNK is a tool for clustering genomes. We refer to the clusters as variable-length-k-mer clusters, or VLKCs. Biologically, these clusters typically represent distinct strains. We refer to subclusters of strains as lineages.

Popscle is a suite of population scale analysis tools for single-cell genomics data.

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment, guppy does all of the downstream analysis of placements, and rppr does useful things having to do with reference packages.

Practical Haplotype Graph (PHG) is a general, graph-based, computational framework that can be used with a variety of skim sequencing methods to infer high-density genotypes directly from low-coverage sequence.

Prinseq is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data.

Prodigal is a tool for fast, reliable protein-coding gene prediction for prokaryotic genome.

PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system CRS to another. This includes cartographic projections as well as geodetic transformations.

Prokka is a pipeline for rapidly annotating prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

Proteinortho is a tool to detect orthologous genes within different species.

ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.

Pullseq is an utility program for extracting sequences from a fasta/fastq file.

purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

pVACtools is a cancer immunotherapy tools suite consisting of pVACseq, pVACbind, pVACfuse, pVACvector, and pVACview.

mpi4py provides a Python interface to MPI or the Message-Passing Interface. It is useful for parallelizing Python scripts.

Pyani is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity.

Pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.