wrf

macrosyntR

R package for comparison of synteny conservation at the genome-wide scale.

odp

oxford dot plots

pyGenomeViz

A genome visualization python package for comparative genomics

Gmove

Gmove is a gene prediction tool

GPS

ancestry

navigator

Graphical user interface for exploring space, time, and taxa in the PBDB

genome_size_vs_protein_count

Shiny app that plots NCBI genomes size versus protein count

maniphono

Python library for the symbolic manipulation of phoneme representations

ielex-data-and-tree

Data and scripts for producing a Baysian phylogenetic tree sample of for the Indo-European family which is "good enough", using data from IELex (Dunn et al. 2011).

SqueezeMeta

A complete pipeline for metagenomic analysis

GENESPACE

scholar.py

A parser for Google Scholar, written in Python

stringtie

Transcript assembly and quantification for RNA-Seq

genometools

GenomeTools genome analysis system.

anvio

An analysis and visualization platform for 'omics data

COPSE

COPSE reloaded public release

EDTA

Extensive de-novo TE Annotator

SRA_Metadata

Get, parse, and extract information from the SRA metadata files

InteractiveComplexHeatmap

Make Interactive Complex Heatmaps

softwipe

Check and score C/C++ software quality

lizard

A simple code complexity analyser without caring about the C/C++ header files or Java imports, supports most of the popular languages.

Liftoff

An accurate GFF3/GTF lift over pipeline

JupiterPlot

A Circos-based tool to visualize genome assembly consistency

GFF3toolkit

Python programs for processing GFF3 files

ComparativeGenomics

"Unravelling the Evolution of Animals" following a Bioinformatics pipeline

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

Broccoli

orthology assignment using phylogenetic and network analyses

multibigwig

A JBrowse plugin for plotting multiple bigwig subtracks

biocode

Bioinformatics code libraries and scripts

tutorials

Tutorials on phylogenetic and phylogenomic inference