wbyu

FasParser

A Windows Graphical Platform for Batch Manipulation of Tremendous Amount of Sequence Data

angsd

Program for analysing NGS data.

GetOrganelle

Get organelle genomes from genome skimming data

GetOrganelleComparison

Examples and comparisons

Beautiful-Visualization-with-R

《R语言数据可视化之美》配套代码

BioGeoBEARS

BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts

covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

FixationSites

The application of R package sitePath on viruses.

gatk

Official code repository for GATK versions 4 and up

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

hyphy-gui

Desktop application for HyPhy

IMa3

IMa3

ipybd

megahit

Ultra-fast and memory-efficient (meta-)genome assembler

ncov

Nextstrain build for novel coronavirus SARS-CoV-2

nextclade

Assign SARS-CoV-2 clades in the browser

orthoscope

An automatic web tool for phylogenetic inference of bilaterian orthogroups under purposeful taxonomic sampling

PhyloSuite

PhyloSuite is an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

sars-like-cov

This is a one-off Nextstrain build for SARS-like coronaviruses

sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences

Sequence-manipulation

A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

TBtools

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

treeman

:deciduous_tree::man: An R package for manipulating phylogentic trees

virmap

wgd

Python package and CLI for whole genome duplication analysis

whaleprep

Nextflow pipeline for preparatory analyses for Whale

wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

wuhan2020-timeline

记录自2019年12月起武汉新冠肺炎疫情进展的时间线。