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Search results for python phylogenomics

phylogenomics x

20 search results found

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.

An analysis and visualization platform for 'omics data

Trifusion ⭐ 61

Streamlining phylogenomic data gathering, processing and visualization

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

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

Aniclustermap ⭐ 38

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

Hybridization detection using phylogenetic invariants

Phylofisher ⭐ 27

PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.

Busco_phylogenomics ⭐ 26

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

Phylociraptor ⭐ 23

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

Phantasm ⭐ 20

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes

Orthosnap ⭐ 16

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

Cafeplotter ⭐ 13

A tool for plotting CAFE5 gene family expansion/contraction result

NGSphy: phylogenomic simulation of next-generation sequencing data

a toolkit for evaluation of the lenght of k-mer in a given genome dataset for alignment-free phylogenimic analysis.

Supermatrix ⭐ 8

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

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Fastdtlmapper ⭐ 7

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

Lescroart2023 ⭐ 7

Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information

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

Hybridization Detection with Convolutional Neural Networks

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