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Search results for python phylogenetics

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56 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

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.

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Vcf2phylip ⭐ 216

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Population-scale genomics

Buddysuite ⭐ 105

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Comparative Genomics Toolkit 3

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

Trifusion ⭐ 61

Streamlining phylogenomic data gathering, processing and visualization

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

Phylopandas ⭐ 39

Pandas DataFrames for phylogenetics

Aniclustermap ⭐ 38

A tool for drawing ANI clustermap between all-vs-all microbial genomes

Nextstrain build for mpox virus

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

Python API for the Interactive Tree of Life (iTOL)

Orthoevolution ⭐ 28

An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵

Busco_phylogenomics ⭐ 26

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Q2 Qemistree ⭐ 24

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Ghost Tree ⭐ 23

creating hybrid-gene phylogenetic trees for diversity analyses

Treesapp ⭐ 22

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

Phylostan ⭐ 21

Phylogenetic inference using Stan

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Chronumental ⭐ 18

Estimating time trees from very large phylogenies

Lineage Designation ⭐ 16

Official place for proposals and details around monkeypox virus lineage designations

Orthosnap ⭐ 16

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Pyphlawd ⭐ 16

Python version of PHLAWD

Python framework for doing ancestral sequence reconstruction

DFOIL: Introgression Testing for Five Taxa

Parallel/Homoplasic SNP Finder

vSNP -- validate SNPs

Wqfm 2020 ⭐ 13

wQFM implementation in Java

Cafeplotter ⭐ 13

A tool for plotting CAFE5 gene family expansion/contraction result

GCtree: phylogenetic inference of genotype-collapsed trees

Phylotoast ⭐ 12

Tools for phylogenetic data analysis including visualization and cluster-computing support.

Automatic evaluation of HGTs

Python Nexus ⭐ 11

python-nexus - Generic nexus (.nex, .trees) reader/writer for python

Pypythia ⭐ 11

Lightweight python library for predicting the difficulty of alignments in phylogenetics

Raxml_ascbias ⭐ 11

Script for removing or counting invariant sites for the RAxML ascertainment bias corrections

Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis

Trisicell ⭐ 9

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

A Python package for converting TEI XML collations to NEXUS and other formats

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Supermatrix ⭐ 8

scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms

Fastdtlmapper ⭐ 7

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

Aphylogeo ⭐ 7

aPhyloGeo is a multiplatform application for the analysis of genetic and climatic conditions.

Taxopedia ⭐ 7

Taxonomic trees (cladograms) from Wikipedia-scraped data.

Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools

Phylovega ⭐ 6

Interactive tree visualizations in Python (powered by Vega).

showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.

Msa_trimmer ⭐ 5

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

A tool for divide-and-conquer tree estimation via a shared distance matrix

Nodefinder ⭐ 5

Tools for node related operations in phylogenetic analyses.

Scphylo Tools ⭐ 5

a python toolkit for single-cell tumor phylogenetic analysis

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