Purdue University

PETSc is a suite of data structures and routines for the scalable parallel solution of scientific applications modeled by partial differential equations.

pggb builds pangenome variation graphs from a set of input sequences.

PHAST is a freely available software package for comparative and evolutionary genomics.

Phd2fasta is a tool to convert Phred ‘phd’ format files to ‘fasta’ format.

PhiPack: PHI test and other tests of recombination

phrap is a program for assembling shotgun DNA sequence data.

phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.

PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies.

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Picrust2 is a software for predicting functional abundances based only on marker gene sequences.

Pilon is an automated genome assembly improvement and variant detection tool.

Pindel is used to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data.

Pirate is a pangenome analysis and threshold evaluation toolbox.

piscem is a rust wrapper for a next-generation index + mapper tool (still currently written in C++17).

pixy is a command-line tool for painlessly estimating average nucleotide diversity within (?) and between (dxy) populations from a VCF.

PlasmidFinder identifies plasmids in total or partial sequenced isolates of bacteria.

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data.

Plink is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.