phylogenetic-tree

There are 1 repository under phylogenetic-tree topic.

YuLab-SMU / tidytree
:shower:A Tidy Tool for Phylogenetic Tree Data Manipulation
phylogenetic-tree cran tree-data tidyverse
Language:R 48
bioinfweb / TreeGraph2
A feature rich and easy to use phylogenetic tree editor
phylogenetic-tree editor metadata phylogenetics bioinformatics nexus nexml phyloxml newick-format
Language:Java 8
Changwanseo / FunIP
Fungal Identification Pipeline
fungi phylogenetic-tree species-delimitation species-identification taxonomy multigene
Language:Python 5
dfornika / tree-with-metadata
Draw a phylogenetic tree, along with a table of metadata
phylogenetics metadata phylogenetic-tree visualization
Language:Python 3
zengxiaofei / busco-tree
A pipeline to construct phylogenetic tree using BUSCOs
busco comparative-genomics phylogenetic-tree
Language:Python 3
Niloth-p / Phylogenetic-Tree-construction-using-Agglomerative-and-Divisive-Hierarchical-clustering
The prog is written to construct the phylogenetic tree (dendrogram) based on DNA/Protein sequences of species given in a dataset using Agglomerative and Divisive Hierarchical Clustering and to compare Agglomerative and Divisive methods
phylogenetic-tree dendrogram hierarchical-clustering agglomerative-clustering divisive-clustering min-linkage needleman-wunsch-algorithm proximity-matrix
Language:Python 2
sirineFoudili / DNA-comparison-and-alignment-
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
dna adn alignement alignment alignment-free indexation bloom-filter k-mers hashing phylogenetic-tree phylogenie dna-alignment needleman-wunsch flask python bioinformatics bioinformatique
Language:JavaScript 2
anicksaha / neighbor_joining
Nei-Saitou neighbor-joining algorithm for phylogeny construction/inference. Neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic/evolutionary trees.
neighbor-joining phylogenetic-tree evolutionary-tree
Language:Python 1
fethalen / orthoquoll
A stand-alone tool for evaluating simple statistics of orthologs
phylogenetics phylogenetic-tree orthology-inference orthology-assignments orthology-relationships orthology
Language:Python 1
kmampent / CacheTD
Implementation of the tree triplet distance algorithms from our paper "Cache oblivious algorithms for computing the triplet distance between trees", published in ESA 2017
algorithm cache-oblivious cachetd phylogenetic-tree triplet triplet-distance
Language:Objective-C 1
pebgroup / Global-plant-diversity
Code and data description to reproduce Tietje et al. (2022) Global variation in diversification rate and species richness are unlinked in plants (https://doi.org/10.1073/pnas.2120662119)
spermatophyta phylogenetic-tree geography species-richness speciation-rates wcvp
Language:R 1
sophiagosselin / tANI_tool
Script for creating a tANI distance matrix for use in phylogenetic reconstruction.
average-nucleotide-identity phylogenetic-data phylogenetic-tree whole-genome-distance
Language:Perl 1
puutools
charlesrocabert / puutools
Easy-to-use C++ library for the live tracking of lineage and coalescence trees in individual-based forward-in-time simulations.
artificial-life-simulations c-plus-plus-library coalescence coalescence-tree evolution-simulation evolutionary-algorithms evolutionary-biology forward-in-time-simulation individual-based-modelling lineage-tracing lineage-tree live-tracking phylogenetic-tree phylogenetics static-library
Language:C++ 0
laelbarlow / sort_seqs_by_clade
Script for sorting FASTA sequences by clade in a given tree topology.
ete3 biopython-library phylogenetic-tree
Language:Python 0
BenbowLab / Benin-NGS
Example files for Benin NGS capacity building project
benin-ngs example ngs-analysis phylogenetic-tree phylogenetics sample-data tutorial vcf-files vcftools
Language:HTML
tomekkorbak / computational-genomics-experiments
A couple of assignments I did for a course in computational (molecular) biology @ University of Warsaw
computational-biology dna-alignment genomics hox-proteins phylogenetic-profiles phylogenetic-tree
Language:Jupyter Notebook

phylogenetic-tree

YuLab-SMU / tidytree

bioinfweb / TreeGraph2

Changwanseo / FunIP

dfornika / tree-with-metadata

zengxiaofei / busco-tree

Niloth-p / Phylogenetic-Tree-construction-using-Agglomerative-and-Divisive-Hierarchical-clustering

sirineFoudili / DNA-comparison-and-alignment-

anicksaha / neighbor_joining

fethalen / orthoquoll

kmampent / CacheTD

pebgroup / Global-plant-diversity

sophiagosselin / tANI_tool

charlesrocabert / puutools

laelbarlow / sort_seqs_by_clade

BenbowLab / Benin-NGS

tomekkorbak / computational-genomics-experiments