The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. It is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

Maxent is a stand-alone Java application for modelling species geographic distributions.

The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

This package provides a converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler). Both hic and cool files describe Hi-C contact matrices.

This tool provides a Python framework to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs. The primary objective of pybio is to simplify genome management. It achieves this by providing automatic download of Ensembl genome assemblies and annotation, provides Python genomic feature search and sequence retrieval from the managed genomes, STAR indexing and mapping and more.

Phylogenetic Analysis with Space/Time models (PHAST) is a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

This library implements a FASTA and a FASTQ parser without relying on a complex dependency tree.

dRep is a Python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

Hotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset. Importantly, "informative" is decided based on how well a gene's variation agrees with some cell metric---some similarity mapping between cells. Genes which are informative are those whose expression varies in similar way among cells which are nearby in the given metric.

The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.

This package provides an R API and htmlwidget facilitating interactive visualization of spatial single-cell data with Vitessce. The R API contains classes and functions for loading single-cell data stored in compatible on-disk formats. The htmlwidget is a wrapper around the Vitessce JavaScript library and can be used in the Viewer tab of RStudio or Shiny apps.

Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

python-cwl-utils provides python utilities and autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.

This package provides string parsing functionalities for generating plotnames, filenames and paths.

ScVelo is a scalable toolkit for RNA velocity analysis in single cells. RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. scVelo generalizes the concept of RNA velocity by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.

Presto is a python toolkit for processing raw reads from high-throughput sequencing of B cell and T cell repertoires.

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

This package provides a Variant Effect Predictor, which predicts the functional effects of genomic variants. It also provides Haplosaurus, which uses phased genotype data to predict whole-transcript haplotype sequences, and Variant Recoder, which translates between different variant encodings.

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.