applications/science/biology

Program for analysing NGS data

Advanced normalization toolkit for medical image registration and other processing

Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences

Tool for estimating an unrooted species tree given a set of unrooted gene trees

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

Detecting natural selection from population-based genetic data

Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants

Suite of tools for addressing questions arising in genomics studies

Powerful toolset for genome arithmetic

Bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already in…

BWK awk modified for biological data

Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences

Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences

Ultrafast memory-efficient short read aligner

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequenc…

Software package for mapping low-divergent sequences against a large reference genome, such as the…

Clustering and comparing protein or nucleotide sequences

General purpose multiple sequence alignment program for protein and DNA/RNA

Computational Morphometry Toolkit

More command-line utilities for working with MINC files

DICOM to NIfTI converter

Tools for exploring deep DNA sequencing data

Structural variant caller for mapped DNA sequenced data

Accelerated BLAST compatible local sequence aligner

Calculate the most likely secondary structure assignment given the 3D structure of a protein

Electronic PCR software tool

Fast genome-wide functional annotation through orthology assignment

European Molecular Biology Open Software Suite

Estimate the unfolded site frequency spectrum and ancestral states

Generic tool for sequence alignment

Collection of Perl and shell scripts for processing MINC files

Ultra-fast all-in-one FASTQ preprocessor

Library and command line interface for interacting with a Flywheel site

Bayesian haplotype-based polymorphism discovery and genotyping

Wide variety of tools with a primary focus on variant discovery and genotyping

Ultra-fast computation of genome mappability

Remote protein homology detection suite

Graph based aligner

Biosequence analysis using profile hidden Markov models

Visualization tool for interactive exploration of genomic datasets

Program to normalize intensity of MINC files

Efficient and versatile phylogenomic software by maximum likelihood

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi …

InterViews graphical library for Neuron

Next-generation genome browser

Fast multiple sequence alignment program

Program for quantifying abundances of transcripts from RNA-Seq data

UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities

K-mer substring space decomposition

Genomic sequence aligner

Multiple alignment of coding sequences

Multiple alignment program for amino acid or nucleotide sequences

Structural variant caller

Ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn…

Motif-based sequence analysis tools

Evolutionary simulation framework

Estimates population size, migration, population splitting parameters using genetic/genomic data

Command-line utilities for working with MINC files

Collection of Perl and shell scripts for processing MINC files

Short read genome assembler

Versatile pairwise aligner for genomic and spliced nucleotide sequences

Ultra fast and sensitive sequence search and clustering suite

Tools for automated registration using the MINC image format

Bayesian Inference of Phylogeny

Suite of tools for diffusion imaging

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences

MRI non-uniformity correction for MINC files

NEST is a command line tool for simulating neural networks

NEST is a command line tool for simulating neural networks

NEST is a command line tool for simulating neural networks

NEST is a command line tool for simulating neural networks

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Simulation environment for empirically-based simulations of neurons and networks of neurons

Medical image registration software

Software for medical image segmentation, bias field correction, and cortical thickness calculation

Management of analyses and data in DNA metabarcoding

Bayesian haplotype-based mutation calling

Phylogenetic Analysis by Maximum Likelihood (PAML)

Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF

Platypus variant caller

Comprehensive update to the PLINK association analysis toolset

Fast, reliable protein-coding gene prediction for prokaryotic genomes

Model-based Analysis for ChIP-Seq

Model-based Analysis for ChIP-Seq

Evaluates genome assemblies by computing various metrics

Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies

Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies

Tool to retrieve approximate repeats from large DNA sequences

SAM/BAM processing tool

Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files

Tools for manipulating SAM/BAM/CRAM format

Tools for manipulating SAM/BAM/CRAM format

GUI for molecular phylogeny

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation