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The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data

<Write a simple description of the tool>

panaroo - an updated pipeline for pangenome investigation

Universal markup converter (repackaged binaries)

Trained model used by Pangolin

Phylogenetic Assignment of Named Global Outbreak LINeages

GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)

FALCON/Unzip tool-suite (originally by Jason Chin)

CLI tools and add-ons for PacBio's core APIs

A minimap2 frontend for PacBio native data formats

pbsv - PacBio structural variant (SV) calling and analysis tools

A commandline utility to search text in PDF files

The Perl programming language interpreter + some libraries

produce Perl code

Self Contained RDBMS in a DBI Driver

cpanm ready distribution of VCFtools Perl libraries

An automated data conversion tool for connecting population genetics and genomics programs

A Comprehensive Suite of Compilers, Libraries and Tools for HPC

A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

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

Include:

Simple, rapid, and statistically efficient test for recombination.

Package of programs for inferring phylogenies

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.

A Bayesian software for phylogentic reconstrunction using mixture models

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset

Phylogenetic estimation using (Maximum) Likelihood

Java tools for working with NGS data in the BAM format

PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

parallel implementation of gzip that exploits multiple processors and multiple cores to the hilt when compressing data

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

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

PIPmiR algorithm - identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.

pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (AKA monomorphic) sites, which are essential for the correct computation of π and dxy.

Command-line utilities to assist in building tools for the Galaxy project

Platon detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. Therefore, Platon analyzes the distribution bias of protein-coding gene families among chromosomes and plasmids.

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Oxford Nanopore Technologies Pod5 File Format Python API and Tools

Pooch manages your remote data files

Adapter removal and demultiplexing of Oxford Nanopore reads

PostgreSQL is a powerful, open source object-relational database system.

PPanGGOLiN : Depicting microbial species diversity via a Partitioned PanGenome Graph

Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it.

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

Rapid annotation of prokaryotic genomes

Accurate protein secondary structure prediction

pyani provides a package and script for calculation of genome-scale average nucleotide identity.

Python software for processing CRAC and CLIP type data.

EGA python client

Standalone program and library to plot beautiful genome browser tracks.

The gtftk suite providing facilities to manipulate genomic annotations in gtf format.

PyPy is a Python interpreter and just-in-time compiler.

GenomicRanges for Python.

Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

A lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data

Sequence Element Enrichment Analysis (SEER), python implementation

Tools for dealing with tree sequences coming to and from SLiM.

Python is an interpreted, high-level, general-purpose programming language. This environment includes most common libraries for data manipulations (Pandas, Numpy), data visualization (Matplotlib, Seaborn, Altair, Plotly and Bokeh) and machine learning (Tensorflow, PyTorch, Scikit).

Python is an interpreted, high-level, general-purpose programming language. This environment includes most common libraries for data manipulations (Pandas, Numpy), data visualization (Matplotlib, Seaborn, Altair, Plotly ad Bokeh) and machine learning (Tensorflow, PyTorch, Scikit).

Python is an interpreted, high-level, general-purpose programming language. This environment includes most common libraries for data manipulations (Pandas, Numpy), data visualization (Matplotlib, Seaborn, Altair, Plotly and Bokeh) and machine learning (Tensorflow, PyTorch, Scikit).

A fully functional terminal in your browser.