Reverse Dependencies of ete3

The following projects have a declared dependency on ete3:

• abutils — Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
• Agatta — Three-item analysis python package
• airpg — A package to automatically access the inverted repeats of archived plastid genomes
• alifedata-phyloinformatics-convert — alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
• ancestralcost — no summary
• aphylogeo — A phylogenetic and geographic analysis tool
• apscale-gui — Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
• BacDiving — Bacdiving accesses the Bacterial Diversity Metadatabase BacDive and provides various visualization options.
• BacterialTyper — no summary
• bad-phylo — Tool for the estimation of the difficulty of phylogenetic placements
• bdms-sim — Tree simulator for birth-death-mutation-sampling (BDMS) processes
• bg — Implementation of Breakpoint Graph data structure
• biobrary — A library for biological computing works
• BioSAK — BioSAK
• bioviper — Enhancements to Biopython for working with biological data
• budgitree — Budgitree newick tree processor
• build-subpfam — Build clade HMMs from a multiple sequence alignment file
• CAMIViz — A collection of tools to visualize CAMI profiling outputs
• CanSNPer-1.1.0 — CanSNPer: A toolkit for SNP-typing using NGS data.
• card-live-dashboard — A dashboard to display antimicrobial resistance data from CARD:Live
• CCMetagen — Microbiome classification pipeline
• cellsystem — An agent-based framework for the simulation of biological cell systems and more.
• cirtap — A CLI to handle PATRIC data from the FTP
• clinc — Cell Lineage from Normalized Covariance
• clovars — Clonal Variability Simulation
• collapse-gtdb-tree — A simple tool to collapse the reference GTDB tree at a scpecific rank
• ContigNet — ContigNet, a deep learning based phage-host interaction prediction tool
• cospar — CoSpar: integrating state and lineage information for dynamic inference
• DeepARG — no summary
• deepbiome — Deep Learning package using the phylogenetic tree information for microbiome data analysis.
• diamond-add-taxonomy — Tools for working with the NCBI taxonomy database (and DIAMOND output)
• dnctree — Distance-based phylogeny inference using a randomised divide-and-conquer method
• draupnir — Ancestral sequence reconstruction using a tree structured Ornstein Uhlenbeck variational autoencoder
• edgehog — Infering ancestral synteny with hierarchical orthologous groups
• emapper2gbk — Build .gbk files starting from eggnog annotation files and genomes (fasta)
• epimuller — Visualize lineages overtime, with phylogentic context, based on viral genomes
• ervsearch — Tool for identifying endogenous retrovirus like regions in a set of sequences
• esmecata — EsMeCaTa: Estimating Metabolic Capabilties from Taxonomy
• eukcc — Check eukaryotic genomes or MAGs for completeness and contamination
• eukfindertest2 — A small demo package
• expam — Metagenomic profiling using a reference phylogeny
• FastOMA — FastOMA - a package to infer orthology information among proteomes
• fcat — Python package for fCAT, a feature-aware completeness assessment tool
• fdog — Feature-aware Directed OrtholoG search tool
• fedot — Automated machine learning framework for composite pipelines
• fedot-example-test — Evolutionary structural learning framework FEDOT
• ficture — Segmentation free factor analysis for sub-micron resolution spatial transcriptomics
• gctree — phylogenetic inference of genotype-collapsed trees
• genomics-data-index — Indexes genomics data (nucleotide variants, kmers, MLST) for fast querying of features.
• gleipnir-tcr — Gleipnir
• groupBug — Clustering heatmap tool for kraken-style reports
• h1s — Feature-aware orthology prediction tool
• hakku — Tool for article clustering based on word counts in titles and keywords.
• hamstr1s — Feature-aware orthology prediction tool
• HAPpy-ABCENTH — no summary
• har2tree — HTTP Archive (HAR) to ETE Toolkit generator
• heist-hemiplasy — Hemiplasy Inference Simulation Tool. For characterising hemiplasy given traits mapped onto a species tree
• historydag — Basic history DAG implementation
• HogProf — Phylogenetic Profiling with OMA and minhashing
• info-cluster — a hierachical clustering algorithm based on information theory
• jcvi — Python utility libraries on genome assembly, annotation and comparative genomics
• kb-analysis — H1 human embryonic stem cells (hESCs) Data Analysis
• kython — Python Library to compute and plot phylogeny Kmer signatures
• linkageMapper — Genomic similarities per region
• living-tree — An efficient toolkit for constructing and processing taxonomic trees (metagenomic reads count, remapping, etc.).
• makura — NCBI Genome downloader
• matreex — Matreex: compact and interactive visualisation of large gene families using hierarchical phylogenetic profiles
• mditre — Microbial Differentibale Temporal Rule Engine
• MetaCHIP — HGT detection pipeline
• MetaCHIP2 — HGT detection pipeline
• MetaDR — MetaDR package
• MetaLogo — MetaLogo is a heterogeneity-aware sequence logo generator and aligner
• metaquant — Quantitative microbiome analysis
• metatree — Visualisation of polyphyletic groups between phylogenetic trees to a reference tree.
• mgt2001 — A small package for MGT 2001 and MGT 2002 use only
• micone — The Microbial Co-occurrence Network Explorer
• mimic-da — no summary
• mob-suite — MOB-suite is a set of tools for finding, typing and reconstruction of plasmids from draft and complete genome assemblies.
• ncbi-db — Collection of scripts that wrap the Entrez Bio python module, to query and download portions of NCBI databases
• ncbi-taxid — no summary
• ngesh — Simulate random phylogenetic trees
• oggmap — extract orthologous maps (short: orthomap) from OrthoFinder output for query species
• omadb — Client to the OMA browser, using the REST API.
• omamer — OMAmer - tree-driven and alignment-free protein assignment to sub-families
• Omark — OMArk - Proteome quality assesment based on OMAmer placements
• omataxonomy — Package to work with combined NCBI and GTDB taxonomy
• orthomap — extract orthomap from OrthoFinder output for query species
• pandoo — Pandoo: a pipeline of tools for bacterial genomics.
• PaReBrick — A bioinf tool for finding genome rearrangements in bacterial genomes
• pastml — Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
• pertpy — Perturbation Analysis in the scverse ecosystem.
• phastSim — Fast sequence evolution simulation for SARS-CoV-2 phylogenies and other genomic epidemiological datasets
• phylodeep — Phylodynamic paramater and model inference using pretrained deep neural networks.
• phylofisher — PhyloFisher is a software package for the creation, analysis, and visualization of phylogenomic datasets that consist of protein sequences from eukaryotic organisms.
• phylogeny — An exploration of algorithms for phylogeny reconstruction.
• phyltr — Unix filters for manipulating and analysing (samples of) phylogenetic trees represented in the Newick format
• PhyNetPy — PhyNetPy is a library to provide not only methods, but a framework for the analysis, inference, simulation, and visualization of phylogenetic networks and trees
• PLoT-ME — Pre-classification of Long-reads for Memory Efficient Taxonomic assignment
• plot-phylo — Module to draw a phylogenetic tree using matplotlib
• prophyle — ProPhyle metagenomic classifier