#

phylogeny

Here are 95 public repositories matching this topic...

bioconvert / bioconvert

Star

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Updated Apr 17, 2020
Python

eaton-lab / toytree

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A minimalist tree plotting library using toyplot graphs

python tree plotting phylogeny

Updated Aug 12, 2021
Jupyter Notebook

YuLab-SMU / treedata-book

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📚 a complete reference book for treeio, tidytree and ggtree packages

visualization data-import data-manipulation phylogeny ggtree tidytree treeio

Updated Aug 14, 2021
HTML

evolbioinfo / gotree

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Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

tree nexus tree-structure newick phylogeny gotree itol

Updated Jun 15, 2021
Go

dereneaton / ipyrad

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Interactive assembly and analysis of RAD-seq data sets

genomics assembly phylogeny rad-seq

Updated Aug 14, 2021
Jupyter Notebook

evolbioinfo / goalign

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Goalign is a set of command line tools and an API to manipulate multiple alignments. It is implemented in Go language.

nexus alignment fasta phylogeny phylip phylip-alignment

Updated Jul 28, 2021
Go

MicrobeTrace

CDCgov / MicrobeTrace

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The Visualization Multitool for Molecular Epidemiology and Bioinformatics

bioinformatics genomics phylogenetic-trees phylogenetics epidemiology network-visualization hiv cdc phylogenomics phylogeny sequence-alignment genomic-data-analysis genomics-visualization pathogens

Updated Aug 13, 2021
HTML

raphael-group / machina

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Framework for Metastatic And Clonal History INtegrative Analysis

sequencing migration phylogeny metastasis comigration polyclonal reseeding monoclonal

Updated Mar 5, 2021
Jupyter Notebook

ropensci / rotl

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Interface to Open Tree of Life API

r taxonomy rstats r-package phylogeny peer-reviewed

Updated Oct 22, 2020
R

bmaitner / RBIEN

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Tools for accessing the Botanical Information and Ecology Network (BIEN) database

r open-science plant ecology traits biodiversity phylogeny botanical range-maps bien

Updated May 6, 2021
HTML

biocore / empress

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Open

Add convenience method to empress.js that gets the 0-based index of a feature metadata column

fedarko commented Aug 12, 2021

We repeat this paradigm a lot in empress.js (five times just using this._featureMetadataColumns, by my count, and I'm pretty sure most of these are my fault :P):

var fmIdx = _.indexOf(this._featureMetadataColumns, cat);
if (fmIdx < 0) {
    throw 'Feature metadata column "' + cat + '" not present in data.';
}

It'd be nice to just make a convenience function for this:

``

Read more

nice to have good first issue refactoring

Open

Separate McHelper into a separate GitHub action from the Main CI

Open

Fix resizing in main legend when coloring tree by feature metadata gradient with non-numeric warning message

Find more good first issues →

nf-core / bactmap

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A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

workflow tree pipeline genomics nextflow mapping bacteria phylogeny bacterial nf-core bacterial-genome-analysis

Updated Jul 27, 2021
Nextflow

ngs-fzb / MTBseq_source

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MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

pipeline genomics ngs variants epidemiology phylogeny tuberculosis

Updated Jul 13, 2021
Perl

prophyle / prophyle

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Accurate, resource-frugal and deterministic DNA sequence classifier.

bioinformatics metagenomics viruses bwt bacteria k-mer phylogeny metagenomic-classification taxonomic-classification

Updated Aug 16, 2021
Python

daijiang / phyr

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Functions for phylogenetic analyses

r bayesian glmm inla phylogeny rpackage species-distribution-modeling

Updated Jun 27, 2021
R

EToKi

zheminzhou / EToKi

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all methods related to Enterobase

assembly mlst spades genotype phylogeny phylo

Updated Jul 26, 2021
Python

Ensembl / treebest

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TreeBeST: Tree Building guided by Species Tree (Ensembl Compara modifications)

reconciliation ensembl neighbor-joining maximum-likelihood phylogeny species-trees gene-trees

Updated Oct 9, 2019
C

khabbazian / l1ou

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Detection of evolutionary shifts in Ornstein-Uhlenbeck models

phylogeny ornstein-uhlenbeck study-trait-evolution evolutionary-shift

Updated Mar 26, 2019
R

ropensci / brranching

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I can haz all the phylogenies

r rstats r-package phylogeny phylogenies

Updated May 11, 2021
R

bediger4000 / malware-phylogeny

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malware phylogeny for WSO web shell, Shellbot IRC bot and algorithm

wso2 malware irc-bot trait web-shell species phylogeny shellbot malware-phylogeny

Updated Mar 24, 2019
Perl

JosephCrispell / homoplasyFinder

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A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

consistency mutations indels phylogeny nucleotide-alignment homoplasy

Updated Jun 2, 2021
R

zachcp / phylocanvas

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htmlwidgets for phylocanvas

r htmlwidgets phylogeny

Updated Dec 3, 2019
R

Colelyman / kleuren

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Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees

bioinformatics phylogenetics de-bruijn-graphs phylogeny

Updated Mar 26, 2019
C++

justincbagley / piranha

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Scripts for file processing and analysis in phylogenetics and phylogeography

shell ssh r snps supercomputer phylogeography bayesian-inference maximum-likelihood population-structure phylogeny

Updated Jan 6, 2021
Shell

PlantPhylomoji

ghuertaramos / PlantPhylomoji

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Dataset and scripts to create a Phylogeny of Plant Emojis

emoji plants phylogenetics phylogeny ggtree

Updated Apr 27, 2021
Jupyter Notebook

jananiravi / compbio-gists

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Computational Biology & Bioinformatics Resources

shell data-science bioinformatics r computational-biology comparative-genomics gists molecular-evolution transcriptomics phylogeny

Updated Mar 19, 2020
Shell

jonchang / fishtree

Sponsor Star

The R interface to the Fish Tree of Life

cran r phylogeny

Updated Aug 16, 2021
R

lmc297 / bactaxR

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Bacterial taxonomy construction and evaluation in R

taxonomy bacteria phylogeny ani average-nucleotide-identity medoid-genomes bacterial-species

Updated Apr 18, 2020
R

tothuhien / lsd2

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A phylogeny dating method using least-squares algorithms and criteria

least-squares dating phylogeny time-scaling

Updated Aug 11, 2021
C++

justincbagley / MAGNET

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Shell script pipeline for inferring ML gene trees for many loci (e.g. genomic RAD loci)

pipeline raxml maximum-likelihood phylogeny gene-trees snp-data inferring-species-trees

Updated Jan 4, 2021
Shell

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