High-precision TE Annotator

Generating UTRs from SHort Reads

Program for aligning DNA sequences, a pairwise aligner.

cTENOR is tool for merging results of TE classify tools

Chromosome-level scaffolding using multiple references

Official home of genome aligner based upon notion of Cactus graphs

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, pr…

An accurate GFF3/GTF lift over pipeline

What the Package Does (One Line, Title Case)

A tool for recovering synteny blocks from multiple alignment

A fast whole-genome aligner based on de Bruijn graphs

Detecting multi-genome synteny using minimizer graph mapping

IsoEM2: fast bootstrap-based estimation of gene and isoform expression using RNA-Seq data

The Generic Mapping Tools

A modular, containerized pipeline for ATAC-seq data processing

ATAC-seq peak-calling and QC analysis pipeline

ENCODE ATAC-seq pipeline

Quickly search, compare, and analyze genomic and metagenomic data sets.

qp and expression data visualisation.

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

RankCompV3: a differential expression analysis algorithm based on the relative expression orderings (REOs) of gene pairs

Genome assembly evaluation tool

Predicting TF sequence-specificity similarity with weighted alignments

RNA secondary structure/sequence profiles for homology search and alignment

Fast Gene Set Enrichment Analysis

Coding-Non-Coding Index (CNCI)

A Python package with integrated lncRNA prediction methods