JiangpingShu's repositories
GetOrganelle
Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
AnchorWave
sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
wgd
Python package and CLI for whole-genome duplication related analyses
pcoc
Convergent substitution detection tool based on the PCOC model
phyx
phylogenetics tools for linux (and other mostly posix compliant) computers
ksrates
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
ALGA
This repository contains code of ALGA - short read de novo genome assembler.
seqmagick
An imagemagick-like frontend to Biopython SeqIO
HTSanalyzeR2
HTSanalyzeR2: A R package for gene set enrichment and network analysis of various high-throughput data
HomBlocks
HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching