Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

pypi.org "phylogenetics" keyword

predsim 0.7.0
Command-line tool for simulating predictive datasets from MrBayes' output.
9 versions - Latest release: almost 5 years ago - 1 dependent repositories - 88 downloads last month - 2 stars on GitHub - 2 maintainers
sc-supertree 2024.5.6
Spectral Cluster Supertree
3 versions - Latest release: 6 days ago - 100 downloads last month - 5 stars on GitHub - 2 maintainers
superrec2 0.1.0
Run and compare algorithms for phylogenetic reconciliation and super-reconciliation
1 version - Latest release: 11 months ago - 19 downloads last month - 5 stars on GitHub - 2 maintainers
Top 7.5% on pypi.org
hyphy-python 0.1.11
HyPhy package interface library
8 versions - Latest release: 12 months ago - 1 dependent package - 2 dependent repositories - 195 downloads last month - 195 stars on GitHub - 3 maintainers
hyphy 0.1.3
HyPhy package interface library
2 versions - Latest release: over 7 years ago - 1 dependent repositories - 6 downloads last month - 194 stars on GitHub - 2 maintainers
Top 1.6% on pypi.org
ete3 3.1.3 💰
A Python Environment for (phylogenetic) Tree Exploration
30 versions - Latest release: about 1 year ago - 69 dependent packages - 309 dependent repositories - 43.2 thousand downloads last month - 752 stars on GitHub - 1 maintainer
sonicparanoid 2.0.5
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and la...
65 versions - Latest release: about 1 month ago - 1 dependent repositories - 895 downloads last month - 4 stars on GitLab.com - 2 maintainers
spruceup 2022.2.4
A module for lexible identification, visualization, and removal of outliers from large multiple s...
8 versions - Latest release: over 2 years ago - 1 dependent repositories - 76 downloads last month - 17 stars on GitHub - 2 maintainers
torchtree 1.0.1
Phylogenetic inference with pytorch
5 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 73 downloads last month - 12 stars on GitHub - 2 maintainers
Top 0.6% on pypi.org
biopython 1.83
Freely available tools for computational molecular biology.
60 versions - Latest release: 4 months ago - 637 dependent packages - 3,405 dependent repositories - 832 thousand downloads last month - 3,908 stars on GitHub - 5 maintainers
mah51-biopython 1.1
Freely available tools for computational molecular biology.
2 versions - Latest release: about 2 years ago - 1 dependent repositories - 28 downloads last month - 3,900 stars on GitHub - 1 maintainer
phykit 1.19.4
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
65 versions - Latest release: 8 days ago - 1 dependent repositories - 1.06 thousand downloads last month - 46 stars on GitHub - 2 maintainers
Top 2.5% on pypi.org
tskit 0.5.6
The tree sequence toolkit.
36 versions - Latest release: 7 months ago - 12 dependent packages - 54 dependent repositories - 8.62 thousand downloads last month - 143 stars on GitHub - 2 maintainers
Top 6.9% on pypi.org
cogent3 2024.2.5a1
COmparative GENomics Toolkit 3: genomic sequence analysis within notebooks or on compute systems ...
20 versions - Latest release: 3 months ago - 2 dependent packages - 5 dependent repositories - 1.69 thousand downloads last month - 93 stars on GitHub - 1 maintainer
orthoevol 0.9.0a2
This package aids in the analysis of orthologous genes.
1 version - Latest release: over 6 years ago - 1 dependent repositories - 10 downloads last month - 27 stars on GitHub - 4 maintainers
Top 1.7% on pypi.org
dendropy 4.6.1
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...
24 versions - Latest release: 11 months ago - 24 dependent packages - 109 dependent repositories - 7.27 thousand downloads last month - 4 maintainers
topiary-asr 0.0.1
Python framework for doing ancestral sequence reconstruction using pandas dataframes and ete3 tre...
1 version - Latest release: almost 2 years ago - 7 downloads last month - 27 stars on GitHub - 2 maintainers
clipkit 2.3.0
Alignment trimming software for phylogenetics.
44 versions - Latest release: 12 days ago - 1 dependent repositories - 728 downloads last month - 52 stars on GitHub - 1 maintainer
phytreeviz 0.2.0
Simple phylogenetic tree visualization python package
2 versions - Latest release: 3 months ago - 61 downloads last month - 25 stars on GitHub - 2 maintainers
Top 9.3% on pypi.org
python-nexus 2.9.0
A nexus (phylogenetics) file reader (.nex, .trees)
44 versions - Latest release: over 1 year ago - 4 dependent packages - 14 dependent repositories - 325 downloads last month - 15 stars on GitHub - 4 maintainers
Top 4.9% on pypi.org
treeswift 1.1.42
TreeSwift: Fast tree module for Python 2 and 3
139 versions - Latest release: about 1 month ago - 8 dependent packages - 17 dependent repositories - 14.5 thousand downloads last month - 69 stars on GitHub - 1 maintainer
beaglepy 0.0.2
Python binding for beagle
2 versions - Latest release: almost 3 years ago - 1 dependent repositories - 22 downloads last month - 1 stars on GitHub - 2 maintainers
phyddle 0.2.0
Software to fiddle around with deep learning for phylogenetic models
7 versions - Latest release: about 1 month ago - 30 downloads last month - 2 stars on GitHub - 4 maintainers
phylophun 0.1.0
phylophun is a python package to help manipulate files to conduct phylogenetic analysis.
1 version - Latest release: almost 4 years ago - 1 dependent repositories - 9 downloads last month - 1 stars on GitHub - 2 maintainers
r2g 1.0.5
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an...
6 versions - Latest release: over 3 years ago - 1 dependent repositories - 59 downloads last month - 49 stars on GitHub - 2 maintainers
qiime-tools 1.1.2
Useful additions to the QIIME analysis pipeline including tools for data visualization and cluste...
3 versions - Latest release: over 9 years ago - 3 dependent repositories - 41 downloads last month - 12 stars on GitHub - 1 maintainer
orthofisher 1.1.0
orthofisher
20 versions - Latest release: 7 months ago - 1 dependent repositories - 187 downloads last month - 24 stars on GitHub - 2 maintainers
phylostan 1.0.5
Phylogenetic inference with Stan
6 versions - Latest release: almost 2 years ago - 1 dependent repositories - 20 downloads last month - 22 stars on GitHub - 1 maintainer
mycorrhiza 0.0.28
Mycorrhiza population assignment tools.
25 versions - Latest release: almost 5 years ago - 1 dependent repositories - 196 downloads last month - 5 stars on GitHub - 2 maintainers
taxoniumtools 2.0.115
Generate files for taxonium
83 versions - Latest release: 4 months ago - 640 downloads last month - 90 stars on GitHub - 1 maintainer
metafitch 0.0.3
"Metadata ancestral state reconstruction by Fitch's method"
3 versions - Latest release: over 1 year ago - 7 downloads last month - 19 stars on GitHub - 2 maintainers
chronumental 0.0.63
Large timetrees
55 versions - Latest release: 6 months ago - 615 downloads last month - 23 stars on GitHub - 1 maintainer
sci-phy 0.1.0
Sci-Phy is a python package for the statistical analysis and modelling of evolved data using phy...
1 version - Latest release: over 2 years ago - 1 dependent repositories - 24 downloads last month - 2 maintainers
teiphy 0.1.11
Converts TEI XML collations to NEXUS and other formats
11 versions - Latest release: 17 days ago - 132 downloads last month - 9 stars on GitHub - 2 maintainers
cytopast 1.1.1
Visualisation of PastML trees.
33 versions - Latest release: over 5 years ago - 1 dependent repositories - 46 downloads last month - 2 stars on GitHub - 2 maintainers
aphylogeo 1.0.0
A phylogenetic and geographic analysis tool
7 versions - Latest release: 5 months ago - 56 downloads last month - 9 stars on GitHub - 2 maintainers
splitspy 0.0.10
Phylogenetic outlines
6 versions - Latest release: over 3 years ago - 1 dependent repositories - 52 downloads last month - 1 maintainer
auto-phylo-pipeliner 1.0.1
A GUI to create auto-phylo pipelines.
2 versions - Latest release: 6 months ago - 28 downloads last month - 0 stars on GitHub - 2 maintainers
sumac 2.0
SUMAC: Supermatrix Constructor
9 versions - Latest release: 9 months ago - 2 dependent repositories - 42 downloads last month - 8 stars on GitHub - 2 maintainers
lexedata 1.0.7
Tools to edit lexical data in CLDF, and transform it to and from other well-known formats.
9 versions - Latest release: over 1 year ago - 1 dependent repositories - 10 downloads last month - 3 stars on GitHub - 4 maintainers
dendropy-calver 2023.330.2
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...
1 version - Latest release: about 1 year ago - 12 downloads last month - 0 stars on GitHub - 2 maintainers
arbow 0.6.0
Cultivate your MSA to get better trees
15 versions - Latest release: about 4 years ago - 1 dependent repositories - 150 downloads last month - 1 maintainer
suchtree 1.0
A python library for doing fast, thread-safe computations on phylogenetic trees
7 versions - Latest release: almost 2 years ago - 1 dependent repositories - 212 downloads last month - 26 stars on GitHub - 2 maintainers
phylopandas 0.8.0
Pandas for phylogenetics
13 versions - Latest release: over 4 years ago - 2 dependent repositories - 128 downloads last month - 69 stars on GitHub - 4 maintainers
datasnakes 0.1.1a1
This package helps in the analysis of orthologous genes.
2 versions - Latest release: over 6 years ago - 1 dependent repositories - 11 downloads last month - 27 stars on GitHub - 2 maintainers
sato 0.1.7
Python package that generates consensus sequence from the forward and reverse sequences, performs...
9 versions - Latest release: 12 days ago - 66 downloads last month - 0 stars on GitHub - 2 maintainers
scphylo-tools 0.0.4
a python toolkit for single-cell tumor phylogenetic analysis
5 versions - Latest release: 10 months ago - 1 dependent repositories - 222 downloads last month - 5 stars on GitHub - 1 maintainer
phylovega 0.3
Interactive Phylogenetic trees in Vega from Python.
3 versions - Latest release: over 4 years ago - 2 dependent repositories - 27 downloads last month - 11 stars on GitHub - 2 maintainers
trifusion 1.0.2
Streamlining phylogenomic data gathering, processing and visualization
35 versions - Latest release: over 5 years ago - 1 dependent repositories - 144 downloads last month - 86 stars on GitHub - 2 maintainers
pastml 1.9.43
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
106 versions - Latest release: 3 months ago - 2 dependent repositories - 573 downloads last month - 24 stars on GitHub - 2 maintainers
pear-ebi 0.1.84
Embeds phylogenetic tree distances and produce representations
87 versions - Latest release: 13 days ago - 846 downloads last month - 2 stars on GitHub - 4 maintainers
taxopedia 1.1.3
Taxonomic trees (cladograms) from Wikipedia-scraped data.
8 versions - Latest release: about 3 years ago - 1 dependent repositories - 45 downloads last month - 7 stars on GitHub - 2 maintainers
bgtools 0.0.1
bgtools: A Python package for managing playing board games
1 version - Latest release: almost 4 years ago - 1 dependent repositories - 22 downloads last month - 1 stars on GitHub - 2 maintainers
buddysuite 1.4.0
BuddySuite is a collection of command line utilities written in Python for working with biologica...
14 versions - Latest release: over 2 years ago - 1 dependent repositories - 83 downloads last month - 121 stars on GitHub - 1 maintainer
Top 7.4% on pypi.org
gtdbtk 2.4.0
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
48 versions - Latest release: 18 days ago - 2 dependent repositories - 403 downloads last month - 430 stars on GitHub - 3 maintainers
phylopypruner 1.2.6
tree-based orthology inference
86 versions - Latest release: about 2 years ago - 1 dependent repositories - 490 downloads last month - 6 stars on GitLab.com - 2 maintainers
treeprofiler 1.2.0
TreeProfiler is command-line tool for profiling metadata table into phylogenetic tree with descri...
3 versions - Latest release: 8 months ago - 33 downloads last month - 24 stars on GitHub - 2 maintainers
baltic 0.2.2
Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees
12 versions - Latest release: 10 months ago - 1 dependent package - 329 downloads last month - 85 stars on GitHub - 4 maintainers
commonnexus 1.9.2
A nexus (phylogenetics) file reader and writer (.nex, .trees)
14 versions - Latest release: 6 months ago - 2 dependent packages - 1 dependent repositories - 1.5 thousand downloads last month - 2 stars on GitHub - 4 maintainers
mapgl 1.3.1
Prediction of lineage-specific gain and loss of sequence elements using phylogenetic maximum pars...
12 versions - Latest release: almost 4 years ago - 1 dependent repositories - 71 downloads last month - 3 stars on GitHub - 2 maintainers
treesapp 0.11.4
TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.
23 versions - Latest release: almost 2 years ago - 1 dependent repositories - 730 downloads last month - 24 stars on GitHub - 2 maintainers
trisicell 0.2.3
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
26 versions - Latest release: 5 months ago - 1 dependent repositories - 1.19 thousand downloads last month - 10 stars on GitHub - 1 maintainer
aniclustermap 1.3.0
A tool for drawing ANI clustermap between all-vs-all microbial genomes
5 versions - Latest release: 6 months ago - 1 dependent repositories - 69 downloads last month - 41 stars on GitHub - 1 maintainer
beastiary 1.8.3
Real time and remote MCMC trace monitoring with BEASTIARY
59 versions - Latest release: 2 months ago - 369 downloads last month - 16 stars on GitHub - 1 maintainer
Top 4.1% on pypi.org
phylo-treetime 0.11.3
Maximum-likelihood phylodynamic inference
40 versions - Latest release: about 2 months ago - 3 dependent packages - 11 dependent repositories - 2.04 thousand downloads last month - 204 stars on GitHub - 3 maintainers
Top 6.2% on pypi.org
itolapi 4.1.4
API for interacting with itol.embl.de
22 versions - Latest release: 4 months ago - 4 dependent packages - 12 dependent repositories - 1.02 thousand downloads last month - 31 stars on GitHub - 2 maintainers
phylomatcher 0.3.2
A tool for parsing and extracting taxon synonyms.
3 versions - Latest release: almost 1 year ago - 22 downloads last month - 2 stars on GitHub - 2 maintainers
cafeplotter 0.2.0
A tool for plotting CAFE5 gene family expansion/contraction result
3 versions - Latest release: 8 months ago - 104 downloads last month - 17 stars on GitHub - 2 maintainers
pyasr 0.6.1
Ancestral sequence reconstruction using Python
5 versions - Latest release: almost 6 years ago - 1 dependent repositories - 55 downloads last month - 11 stars on GitHub - 2 maintainers
phyplot 0.1.0
PhyloGrpah is a python package for plotting evolutionary trees and data.
1 version - Latest release: about 1 year ago - 18 downloads last month - 2 maintainers
orthosnap 1.3.0
orthosnap, identify orthologous subgroups of genes in large orthologous groups of genes.
8 versions - Latest release: 5 months ago - 1 dependent repositories - 105 downloads last month - 18 stars on GitHub - 2 maintainers
ncbitaxonomy 3.1.2
The basic NCBI taxonomy functionality from ETE3
4 versions - Latest release: about 3 years ago - 1 dependent repositories - 46 downloads last month - 2 maintainers
getphylo 0.2.1
a python package for automated generation of heuristic phylogenetic trees from genbank files
7 versions - Latest release: 3 months ago - 46 downloads last month - 13 stars on GitHub - 2 maintainers
python_cipres 0.9
CIPRES REST API Client
5 versions - Latest release: about 8 years ago - 2 dependent repositories - 16 downloads last month - 1 maintainer
torchtree-scipy 1.0.0
Plugin for using scipy in torchtree
1 version - Latest release: 6 months ago - 12 downloads last month - 1 stars on GitHub - 2 maintainers
phylogemetric 1.2.2
A python library for calculating the delta score (Holland et al. 2002) and Q-Residual (Gray et al...
11 versions - Latest release: about 2 years ago - 3 dependent repositories - 80 downloads last month - 4 stars on GitHub - 2 maintainers
phylorank 0.1.12
Assigns taxonomic ranks based on evolutionary divergence.
25 versions - Latest release: about 2 years ago - 3 dependent repositories - 83 downloads last month - 21 stars on GitHub - 4 maintainers
ab12phylo 0.5.21b0
Integrated pipeline for ML phylogenetic inference from ABI trace and FASTA data
8 versions - Latest release: over 2 years ago - 1 dependent repositories - 83 downloads last month - 3 stars on GitHub - 1 maintainer
ancestralcost 1.0.1
Calculate the parsimony cost of having an ancestral residue implied by an alignment and tree
2 versions - Latest release: over 2 years ago - 1 dependent repositories - 26 downloads last month - 1 stars on GitHub - 2 maintainers
splitp 0.1.8 💰
Phylogenetic tools and methods involving splits and matrix rank
8 versions - Latest release: about 2 years ago - 1 dependent repositories - 43 downloads last month - 1 stars on GitHub - 2 maintainers
bacpage 2024.3.8
An easy-to-use pipeline for the assembly and analysis of bacterial genomes
3 versions - Latest release: 2 months ago - 20 downloads last month - 7 stars on GitHub - 2 maintainers
ngesh 1.2.1
Simulate random phylogenetic trees
13 versions - Latest release: almost 2 years ago - 1 dependent repositories - 89 downloads last month - 9 stars on GitHub - 2 maintainers
ratecounter 1.1
ratecounter - Nexus file rate counter for language phylogenies
2 versions - Latest release: over 5 years ago - 1 dependent repositories - 27 downloads last month - 0 stars on GitHub - 2 maintainers
phylotoast 1.3.0
Tools for phylogenetic data analysis including visualization and cluster-computing support.
1 version - Latest release: about 8 years ago - 2 dependent repositories - 18 downloads last month - 12 stars on GitHub - 1 maintainer
phydms 2.4.1
Phylogenetic analyses informed by deep mutational scanning data.
36 versions - Latest release: about 3 years ago - 3 dependent repositories - 105 downloads last month - 14 stars on GitHub - 2 maintainers
sgtree 0.0.10
Computational pipeline for fast and easy construction of phylogenetic trees.
1 version - Latest release: over 3 years ago - 1 dependent repositories - 5 downloads last month - 2 maintainers
phylosequel 0.0.2
Toolkit and library for BioSQL database interaction and operations.
2 versions - Latest release: about 15 years ago - 1 dependent repositories - 7 downloads last month - 1 maintainer
phonechars 0.1
Extract phonological phylogenetic characters from aligned data
1 version - Latest release: over 1 year ago - 16 downloads last month - 1 stars on GitHub - 2 maintainers
panphylo 0.3
A tool for converting and manipulating phylogenetic data
3 versions - Latest release: almost 2 years ago - 1 dependent repositories - 18 downloads last month - 0 stars on GitHub - 2 maintainers
ebg 0.12.0
Tool for estimating the Felsenstein Bootstrap support of phylogenetic trees
4 versions - Latest release: 5 months ago - 14 downloads last month - 1 stars on GitHub - 1 maintainer
treemaker 1.0.3
A python tool for generating a Newick formatted tree from alist of classifications
6 versions - Latest release: over 5 years ago - 3 dependent repositories - 19 downloads last month - 7 stars on GitHub - 1 maintainer
pglt v0.1-beta
pG-lt: An automated pipeline for phylogeney generation.
1 version - Latest release: about 9 years ago - 2 dependent repositories - 10 downloads last month - 3 stars on GitHub - 1 maintainer
pyphylogenomics 0.3.12
Tools to work in phylogenomics, from NSG group http://nymphalidae.utu.fi
14 versions - Latest release: over 10 years ago - 1 dependent repositories - 19 downloads last month - 10 stars on GitHub - 2 maintainers
treesimulator 0.1.9
Simulation of rooted phylogenetic trees under a given Multitype Birth–Death model.
13 versions - Latest release: 4 months ago - 1 dependent repositories - 6 downloads last month - 0 stars on GitHub - 2 maintainers
phasty 0.5.3
A Python interface for PHAST (phylogenetic analysis with space/time models).
8 versions - Latest release: 6 months ago - 5 downloads last month - 0 stars on GitHub - 2 maintainers
heist-hemiplasy 0.3.1
Hemiplasy Inference Simulation Tool. For characterising hemiplasy given traits mapped onto a spec...
1 version - Latest release: about 4 years ago - 1 dependent repositories - 7 downloads last month - 5 stars on GitHub - 1 maintainer
fastdtlmapper 0.3.4
Fast genome-wide DTL(Duplication-Transfer-Loss) event mapping tool
7 versions - Latest release: over 1 year ago - 1 dependent repositories - 34 downloads last month - 10 stars on GitHub - 1 maintainer
vsnpdev 0.0.21
USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Bruc...
19 versions - Latest release: over 4 years ago - 1 dependent repositories - 26 downloads last month - 16 stars on GitHub - 2 maintainers
jplaceparser 0.0.2
Tools to parse the JPLACE files
2 versions - Latest release: over 1 year ago - 5 downloads last month - 2 stars on GitHub - 2 maintainers
treesnake 0.1.0
TreeSnake is a python package for inferring evolutionary trees
1 version - Latest release: over 2 years ago - 1 dependent repositories - 5 downloads last month - 2 maintainers
Related Keywords
bioinformatics 40 python 33 evolution 23 genomics 14 biology 14 phylogenomics 12 phylogeny 12 visualization 10 phylogenetic-trees 9 taxonomy 8 tree 8 orthology 8 genetics 6 computational-biology 6 orthology-inference 5 alignment 5 biopython 5 sequence-alignment 5 molecular-evolution 5 population genetics 5 phylogeography 5 newick 5 evolutionary-biology 4 pbs 4 nexus 4 microbial-genomics 4 comparative-genomics 4 orthologs 3 orthologues 3 evolutionary 3 systematics 3 maximum-likelihood 3 data-science 3 splitstree 3 protein 3 dna 3 phylodynamics 3 visualisation 3 algorithms 3 pipeline 3 science 3 pandas 3 single-cell 3 tree visualization 3 gui 2 microbial ecology 2 QIIME 2 fast 2 single cell 2 paup 2 matplotlib 2 phyloinformatics 2 population 2 bacteria 2 coalescent 2 cancer 2 phylogenies 2 shell 2 sge 2 qsub 2 simulation 2 c-plus-plus 2 beast2 2 trees 2 PASTML 2 phylogenetic-analysis 2 timetree 2 numpyro 2 jax 2 newick-format 2 orthology-assignments 2 slurm 2 qiime 2 microbiome-analysis 2 metagenomics 2 tumor phylogeny 2 microbiome 2 hpc 2 cross-platform 2 16s 2 microbiology 2 16S 2 statistical-methods 2 tree reconstruction 2 tree comparison 2 phylogenomic 2 machine-learning 2 orthology inference 2 variational 2 Bayes 2 pytorch 2 variational-inference 2 protein-structure 2 mrbayes 2 biosql 2 blast 2 ftp 2 bash 2 ncbi 2 wikipedia 1