324 Open source projects that are alternatives of or similar to mcscan

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Python package and CLI for whole-genome duplication related analyses

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Federating genomes with love (and synteny derived from functional annotations)

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

An interactive web portal for exploring immuno-oncology data

dysgu-SV is a collection of tools for calling structural variants using short or long reads

The Ensembl Compara Perl API and SQL schema

Assembling the cause of phenotypes and genotypes from NGS data

Manuscript for functional prediction of transcriptomic “dark matter” across species

My collection of light bioinformatics analysis pipelines for specific tasks

Simple pure Python SAM parser and objects for working with SAM records

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Toolkit for preparing genomes for submission to NCBI

Compute N50/NG50 and auN/auNG

A simple command-line tool to download data from Joint Genome Institute databases

Introduction to Cloud Computing for Genomics

Ploidy agnostic phasing pipeline and algorithm

A modular annotation tool for genomic variants

pythonic wrapper for htslib

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

An open-access bioinformatics text

Complex structural variant detection from WGS data

Clustering scRNAseq by genotypes

Data Wrangling and Processing for Genomics

Bystro genetic analysis (annotation, filtering, statistics)

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Fast alignment and preprocessing of chromatin profiles

PERF is an Exhaustive Repeat Finder

Version 2.1.0 released

Редактируемая статья для блога: систематизация информации по симуляции эволюции

An ontology of cell types

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Simulation of life & evolution

A faster lmm for GWAS. Supports GPU backend.

(WIP) best-practices workflow for rare disease

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

Find causal cell-types underlying complex trait genetics

Chanjo provides a better way to analyze coverage data in clinical sequencing.

A package for designing compact and comprehensive capture probe sets.

Environmental DNA metabarcoding taxonomic identification

Provide R access to the NCI Genomic Data Commons portal.

Write DB migrations with SQL and run them with a CLI

Cutting Edge UI Components for Modern Developers

Genetic maps in autopolyploids

A curated list of awesome bioinformatics software.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

A proof of concept of RNAseq pipeline

A public python implementation of the DeepHyperNEAT system for evolving neural networks. Developed by Felix Sosa and Kenneth Stanley. See paper here: https://eplex.cs.ucf.edu/papers/sosa_ugrad_report18.pdf

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

Genetic Map Comparison

Fast hash function for DNA sequences

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

echt rapid variant annotation and filtering

Inference of switch-like differential expression along single-cell trajectories