Reverse Dependencies of dendropy

The following projects have a declared dependency on dendropy:

• albatradis — Comparitive transposon mutagenesis experiment analysis
• alifedata-phyloinformatics-convert — alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
• aphylogeo — A phylogenetic and geographic analysis tool
• ariba — ARIBA: Antibiotic Resistance Identification By Assembly
• captain-project — Conservation Area Prioritization Through Artificial INtelligence
• cathpy — CathPy - Python Bioinformatics Toolkit for CATH (Protein Classification).
• checkm-genome — Assess the quality of putative genome bins.
• cluster-depp-test — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
• depp — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
• depp-test — DEPP: Deep Learning Enables Extending Species Trees using Single Genes
• DL4Phylo — Deep Learning techniques applied to Phylogenetic Analysis
• easy-amplicon — Add your description here
• Espalier — Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests
• FastaDist — Package to calculate a distance matrix from a multiple sequence file
• FastOMA — FastOMA - a package to infer orthology information among proteomes
• fishlifetraits — no summary
• ggi — no summary
• graftm — GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets
• gtdb-itol-decorate — Creates iTOL files for tree decoration, given a set of GTDB genomes.
• gtdb-validation-tk — A toolbox for validating the GTDB taxonomy.
• gtdblib — An abstraction of objects, files, and third-party tools used by the GTDB. Not intended for public use.
• gtdbtk — A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
• hstrat — hstrat enables phylogenetic inference on distributed digital evolution populations
• magna — Magna is a collection of commands that I frequently use in bioinformatics and day-to-day life.
• magus-msa — Multiple Sequence Alignment using Graph Clustering
• masterpy — Python wrapper to simulate under phylogenetic SIR models using MASTER
• mditre — Microbial Differentibale Temporal Rule Engine
• MetaCHIP2 — HGT detection pipeline
• MetaLogo — MetaLogo is a heterogeneity-aware sequence logo generator and aligner
• MetaPhlAn — MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
• metatree — Visualisation of polyphyletic groups between phylogenetic trees to a reference tree.
• mirmap — Comprehensive prediction of microRNA target repression strength
• ngsphy — phylogenomic simulation of NGS data
• omadb — Client to the OMA browser, using the REST API.
• pandas-charm — A small Python library for getting character matrices (alignments) into and out of pandas
• parnas — Representative taxon sampling from phylogenetic trees
• phylo_utils — Phylogenetics calculations in python
• phylodm — Efficient calculation of phylogenetic distance matrices.
• PhyloJunction — A Python environment for protopying, simulating, and learning with evolutionary models
• phylopandas — Pandas for phylogenetics
• PhyloPhlAn — Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
• phylorank — Assigns taxonomic ranks based on evolutionary divergence.
• phylostan — Phylogenetic inference with Stan
• Physcraper — Physcraper
• predsim — Command-line tool for simulating predictive datasets from MrBayes' output.
• pylabeledrf — A package to compute the Robinson Fould distance extended to labeled topologies.
• qtlsearch — Uses OMA's HOGs to predict genes related to QTL.
• rtd-phylogeny — Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method
• sparg — A package to estimate dispersal rates and locate genetic ancestors from tree sequences
• specify-lmpy — Package of commonly used and shared Lifemapper objects and tools
• SuchTree — A python library for doing fast, thread-safe computations on phylogenetic trees
• tact — Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using taxonomy simulated with birth-death models
• taxtastic — Tools for taxonomic naming and annotation
• torchtree — Phylogenetic inference with pytorch
• torchtree-physher — Phylogenetic inference with pytorch and physher
• treeCl — Phylogenetic Clustering Package
• TreeSAK — BioSAK
• TreeSort — Virus reassortment inference software.Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
• witch-msa — WITCH - A Multiple Sequence Alignment Tool
• wLogDate — Log Transformation Improves Dating of Phylogenies