A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

一些关于基因组及转录组的知识

AlleleFinder is a tool for identifying allele genes from polyploid genome.

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

ggideogram is a ggplot2 extension package for drawing chromosome diagrams

Genome size estimation from long read overlaps

A simple visualisation tool for Multiple Sequence Alignment.

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Calculator for statictics including Theta, D, H, and so on, based on the VCF input.

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

High-precision TE Annotator

GenMap - Fast and Exact Computation of Genome Mappability

a broadly applicable tool for automated gene identification and retrieval

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

A more efficient quality control tool for sequencing data

This perl script calculates the CHI statistic and Fst, as well as launches an external XPEHH program.

Fast Neighbor-Joining and other distance-based methods for phylogenetics

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

Building SuperTranscripts: A linear representation of transcriptome data

The Analysis and Annotation Toolkit

Chunks large genome

genetic variant expressions, annotation, and filtering for great good.

A balanced predictor of protein subcellular localisation in Eukaryotes

Robust individual and aggregate checksums for nucleotide sequences

Python programs for processing GFF3 files