Computational Biology Tools

GADMA (Genetic Algorithm for Demographic Model Analysis) is a Python command-line tool that uses genetic algorithms and Bayesian optimization to automatically infer the demographic history of multiple populations from allele frequency spectrum (AFS) or VCF data, supporting up to three populations and multiple inference engines including dadi and moments.

Scalable gVCF merging and joint variant calling for population sequencing projects.

Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

A new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons.

Hail is a scalable, cloud-native genomic analysis tool designed for large datasets. It provides a query language for genomic data and supports batch computing for efficient variant calling and other analyses.

Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.

AlphaFold 3 is an advanced artificial intelligence system for predicting the 3D structures and interactions of biological molecules. It was developed by DeepMind in collaboration with Isomorphic Labs. It is the successor to AlphaFold 2, which revolutionized protein structure prediction.

AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals. By performing sensitive sequence alignment for each shorter interval via a 2-piece affine gap cost strategy and merging them together, AnchorWave generates a whole-genome alignment for each collinear block. AnchorWave implements commands to guide collinear block identification with or without chromosomal rearrangements and provides options to use known polyploidy levels or whole-genome duplications to inform alignment.

Cell Ranger is a set of analysis pipelines for processing Chromium single cell data. It performs barcode processing and UMI counting to quantify gene expression (from 3', 5', and Flex assays), assembles V(D)J immune receptor sequences, and analyzes Feature Barcode data for applications such as cell surface protein analysis and sample multiplexing.

Cell Ranger ARC is an advanced analytical suite designed for the Chromium Single Cell Multiome ATAC + Gene Expression sequencing. It provides in-depth analysis of gene expression and chromatin accessibility at a single cell level, uniquely linking these aspects for enhanced genomic understanding.

Cell Ranger ATAC is a set of automated analysis pipelines developed by 10x Genomics to process and analyze Chromium Single Cell ATAC (Assay for Transposase-Accessible Chromatin) data. It transforms raw sequencing data (FASTQ files) into insights about chromatin accessibility at the single-cell level.

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing.

Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.

A tool for quick quality assessment of cram and bam files, intended for long read sequencing.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang. Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts.

GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files.

fwdpy11 is a Python package for forward-time population genetic simulation, using a C++ back-end (fwdpp) for efficiency. It supports flexible modelling of selection, demography, and multiple populations, with custom temporal samplers for analyzing populations during simulation.

gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.

Tool for interactive bioimage classification, segmentation and analysis.

riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.