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abpoa

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

andi

♥ Efficient Estimation of Evolutionary Distances

augur

Pipeline components for real-time phylodynamic analysis

bamtools

C++ API & command-line toolkit for working with BAM data

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

biopython

Official git repository for Biopython (originally converted from CVS)

brian2

Brian is a free, open source simulator for spiking neural networks.

daligner

Find all significant local alignments between reads

dazz_db

The Dazzler Data Base

dcmstack

DICOM to Nifti conversion with meta data preservation

dipy

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

e-mem

E-MEM: efficient computation of maximal exact matches for very large genomes

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

fast5

A C++ header-only library for reading Oxford Nanopore Fast5 files

filtlong

quality filtering tool for long reads

flye

De novo assembler for single molecule sequencing reads using repeat graphs

hh-suite

Remote protein homology detection suite.

hnswlib

Header-only C++/python library for fast approximate nearest neighbors

htslib

C library for high-throughput sequencing data formats

insilicoseq

:rocket: A sequencing simulator

ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

jellyfish

A fast multi-threaded k-mer counter

kineticstools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

kleborate

libleidenalg

C++ library of Leiden algorithm

libxdf

C++ library for loading XDF files

math--matrixreal

Matrices of real numbers in Perl

mce-perl

Many-Core Engine for Perl

nitime

Timeseries analysis for neuroscience data

nixpy

Python library for NIX