DENG Ziqi's repositories
auto-fill_horarios
fill tedious register horarios with one line
bigtree
Tree Implementation for Python, integrated with Python list, dictionary, and pandas DataFrame.
biom-format
The Biological Observation Matrix (BIOM) Format Project
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
esmfold_playgroud
just to play esmfold
ete
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
ete-data
Data files to use with the ETE Toolkit
ete4-build
ete4-build with nextflow
ete4-explore
ete4 explore to generate tree img
export2graphlan
Conversion software tool for producing both annotation and tree files for GraPhlAn
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
GTDB-id-convertor
convert GCA id to GCF id in GTDB
GToTree
A user-friendly workflow for phylogenomics
MAPLE
MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.
opentree
Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees
Pear-EBI
Calculates distances of trees in large collections. Embeds distances and plot the embeddings with dynamic interfaces.
peptides.py
Physicochemical properties, indices and descriptors for amino-acid sequences.
pertpy
Perturbation Analysis in the scverse ecosystem.
PhyloToolkit
A command-line tool to generator random phylogenetic tree with given list of names or tips number
ProgrammingAssignment2
Repository for Programming Assignment 2 for R Programming on Coursera
pygbif
GBIF Python client
TreeProfiler
tree visualization for tree + annotation data
treeprofiler_demo
fast demo for treeprofiler 2024
treeprofiler_gallery
treeprofiler_gallery
veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes