54 dependents
| Package | Description | Downloads/month |
|---|---|---|
| hstrat enables phylogenetic inference on distributed digital evolution populatio... | 39K | |
| Virus discovery | 21K | |
| A Swiss-Army-Knife for manipulating phylogenetic trees | 17K | |
| MetaCHIP2 | 7K | |
| Fungal Validation and Identification Pipeline | 4K | |
| A Python library for fast, thread-safe computations on phylogenetic trees | 4K | |
| A toolkit for assigning objective taxonomic classifications to bacterial and arc... | 3K | |
| Precise phylogenetic analysis of microbial isolates and genomes from metagenomes | 3K | |
| An abstraction of objects, files, and third-party tools used by the GTDB. Not in... | 2K | |
| Efficient calculation of phylogenetic distance matrices. | 2K | |
| Tools for taxonomic naming and annotation | 2K | |
| Assess the quality of putative genome bins. | 2K | |
| Clustering phylogenetic trees with python | 2K | |
| GraftM is a pipeline used for identifying and classifying marker gene reads from... | 1K | |
| FastOMA is a scalable software package to infer orthology relationship. | 1K | |
| Tools for working with OrthoXML files. | 1K | |
| Phylogenetics calculations in python | 913 | |
| This package contains the programs that design primer set for microbiological an... | 853 | |
| Taxonomic addition for complete trees: Adds tips to a backbone phylogeny using t... | 728 | |
| Modular Amplicon Sequencing Analysis TOokit | 679 | |
| A phylogenetic and geographic analysis tool | 562 | |
| Multiple Sequence Alignment using Graph Clustering | 497 | |
| Pandas DataFrames for phylogenetics | 495 | |
| NGSphy: phylogenomic simulation of next-generation sequencing data | 483 | |
| WITCH - A Multiple Sequence Alignment Tool | 481 | |
| A probabilistic framework in PyTorch for phylogenetic models | 412 | |
| Add your description here | 411 | |
| Command-line tool for simulating predictive datasets from MrBayes' output. | 410 | |
| TIPP3 and TIPP3-fast: new phylogeny-based metagenomic profiling and taxonomic id... | 368 | |
| Software for phylogenetic model exploration with deep learning | 342 | |
| B- and T-cell receptor sequence annotation, simulation, clonal family and germli... | 326 | |
| 306 | ||
| Creates iTOL files for tree decoration, given a set of GTDB genomes. | 279 | |
| Plot dendropy trees | 259 | |
| Create standalone HTML reports for tracking SNP clusters within NCBI Pathogen De... | 240 | |
| Return time distribution (RTD) based alignment-free phylogeny | 233 | |
| Virus reassortment inference software. Infers both recent and ancestral reassort... | 206 | |
| A Python environment for protopying, simulating, and learning with evolutionary ... | 195 | |
| A package to compute the Robinson Fould distance extended to labeled topologies. | 193 | |
| Phylogenetic inference using Stan | 178 | |
| Microbial Differentibale Temporal Rule Engine | 169 | |
| Comparative TraDIS analysis | 163 | |
| Deep Learning techniques applied to Phylogenetic Analysis | 140 | |
| Python wrapper to simulate under phylogenetic SIR models using MASTER | 130 | |
| Phylogenetic inference with pytorch and physher | 120 | |
| 117 | ||
| High-resolution, noninvasive single-cell lineage tracing based on DNA methylatio... | 114 | |
| Uses OMA's HOGs to predict genes related to QTL. | 110 | |
| Aggregate Linguistic Analysis of Speech Transcripts for Research | 102 | |
| Automatic pre-curation of GTDB trees. | 99 |
