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