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Search results for phylogenetics
phylogenetics
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158 search results found
Whale.jl
⭐
10
Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation
Bioinformatics Toolbox
⭐
10
Docker container for bioinformatics tools and pipelines
Grampa
⭐
10
Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis
Elynx
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9
Analyze, modify and simulate molecular sequence data and phylogenetic trees in a reproducible way.
Ncov Clades Schema
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9
Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain
Cdao
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9
Comparative Data Analysis Ontology - A formalization of concepts and relations relevant to evolutionary comparative analysis
Trisicell
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9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
Rappas
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9
Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Graphphylo
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9
visualization of phylogenetic output files
Light_phylogeny
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9
Light phylogeny API for Rust
Clockor2
⭐
9
Inferring global and local strict molecular clocks using root-to-tip regression
Supermatrix
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8
scripts to process, join, split, or add new proteins to a supermatrix alignment using hmms
Teiphy
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8
A Python package for converting TEI XML collations to NEXUS and other formats
Course R Mol Data
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8
R is nowadays probably the most powerful tool for calculations of all kinds. There are plenty of modules available for work with molecular data. Those will be introduced during the course.
Sensiphy
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8
R package to perform sensitivity analysis for comparative methods
Thirdkind
⭐
8
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconcillation levels
Rncl
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8
An R interface to the Nexus Class Library (C++) to read in quickly large phylogenetic trees and data
Kleuren
⭐
8
Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees
Newicktree.jl
⭐
8
Newick formatted (phylogenetic) trees
Phylogenetics
⭐
8
CRAN Task View: Phylogenetics
Captus
⭐
8
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Treebase
⭐
7
Source code for TreeBASE web application and database
Torchtree
⭐
7
A probabilistic framework in PyTorch for phylogenetic models
Taxopedia
⭐
7
Taxonomic trees (cladograms) from Wikipedia-scraped data.
Supertreebase
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7
Analysis of TreeBASE data through the NeXML API
Linearham
⭐
7
A Bayesian Phylo-HMM for B cell receptor sequence analysis
Fastdtlmapper
⭐
7
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
Scarlet
⭐
7
SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.
Aphylogeo
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7
aPhyloGeo is a multiplatform application for the analysis of genetic and climatic conditions.
Phylovega
⭐
6
Interactive tree visualizations in Python (powered by Vega).
Daisieprep
⭐
6
Extracts phylogenetic island community data from phylogenetic trees
Phylter
⭐
6
Detection of outlier genes and species in phylogenomics
Aphylo
⭐
6
Statistical inference of genetic functions in phylogenetic trees
Hmmufotu
⭐
6
An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
Quartet
⭐
6
R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)
Showtree
⭐
6
showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
Lvb
⭐
6
LVB phylogeny reconstruction software.
Mcphylo.jl
⭐
6
(Hierarchical) Phylogenetic Models in Julia
Phylodiv
⭐
6
Phylogenetic Biodiversity Query Tools
Phyloxml Js
⭐
6
phyloxml.js is a JavaScript program for reading (SAX style parser) and writing phylogenetic trees in phyloXML format.
Nltt
⭐
6
Repository for the R nLTT package
Phylogenies.jl
⭐
6
The BioJulia package for working with phylogenetic trees and geneologies.
Phylohmc
⭐
6
Hamiltonian Monte Carlo on the space of phylogenies
Miapa
⭐
6
Minimum Information About a Phylogenetic Analysis (MIAPA) vocabularies and tools
Nowellpack
⭐
6
Blang library for cancer genomics
Treelikeness
⭐
6
Developing a statistic to test tree likeness and identify genes that don't fit the model.
Microbetrace
⭐
5
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
Treegraph2
⭐
5
A feature rich and easy to use phylogenetic tree editor
Njmerge
⭐
5
A tool for divide-and-conquer tree estimation via a shared distance matrix
Mycorrhiza Algorithm
⭐
5
Combining phylogenetic networks and Random Forests for prediction of ancestry from multilocus genotype data
Coelacanthevolution
⭐
5
Analyses of coelacanth morphometrics, disparity, phylogeny, and rate of evolution
Nodefinder
⭐
5
Tools for node related operations in phylogenetic analyses.
Treesearch
⭐
5
R package for phylogenetic tree search under custom optimality criteria
Scphylo Tools
⭐
5
a python toolkit for single-cell tumor phylogenetic analysis
Scistreer
⭐
5
R/Rcpp implementation of the ScisTree algorithm
Fabaceae_phylogenomics_workflow
⭐
5
Target-enrichment data processing in legumes
Msa_trimmer
⭐
5
Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
Tatajuba
⭐
5
Identification and classification of homopolymeric tracts from reads.
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Python Phylogenetics (74)
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