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1kp_plastid

Plastid phylogenomics scripts and data for Gitzendanner et al. 2018 AJB paper

aegean

Integrated toolkit for analysis and evaluation of annotated genomes

angsd

Program for analysing NGS data.

arachis

Analyzing ReArrangements with Circular Headed Incomplete Sequences

astral

Accurate Species TRee ALgorithm

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

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

bioinformatics-training

Bioinformatics training resources

cgatpipelines

Collection of CGAT NGS Pipelines

chloroseq

a bioinformatic pipeline to systematically analyse the chloroplast transcriptome using RNA-Seq

covariants

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

embl_gene_extractor

Python script to extract gene sequences from embl files

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

f4

Assessing confidence in introgression among four populations

fasconcat-g

FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences. FASconCAT-G implemented process options can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.

fasparser

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

fixationsites

The application of R package sitePath on viruses.

gatk

Official code repository for GATK versions 4 and up

genomescope

Fast genome analysis from unassembled short reads

genometools

GenomeTools genome analysis system.

genomicconsensus

PacBio® variant and consensus caller

getorganelle

Get organelle genomes from genome skimming data

getorganellecomparison

Examples and comparisons

gffread

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

ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

hgt_pnas_2016

homblocks

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

hybpiper

Recovering genes from targeted sequence capture data

hyde

Hybridization detection using phylogenetic invariants