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aiphylo

machine learning for phylogenetics

anc_estimation

animal_tree_root

augur

Pipeline components for real-time phylodynamic analysis

auspice

Web app for visualizing pathogen evolution

bacterialq

Q matrices for bacteria

benchmarkalignments

Benchmark empirical datasets for phylogenetic method development

bioconda-recipes

Conda recipes for the bioconda channel.

chroloplast-genome-assembly

A pipeline for assemble chroloplast genome using short/long reads

cladistic-data

A data store for cladistic data matrices I'm using in my research. Feel free to fork or make pull requests if I've made any errors

communitree

analysis of community assembly using phylogenetics in R

comparison-of-neighbour-joining-software

concordance-factor

Data for concordance factor analysis

concordance_vectors

scripts to calculate and plot concordance vectors

epistemic-landscapes

Simulating the exploration of Epistemic Landscapes

euc_qc

quality control shell scripts for mapping short-read sequencing data to distant reference genomes

eucbase

a database of life history traits, occurrence data, and environmental traits for eucalypts

gap_trees

signal in the gaps?

genome_size_in_plants

genome size evolution in plants

ghost

gtdb_trees

Application of pandemic-scale tools for building the GTDB tree

hmms

hidden markov models for phylogenetics

html5_genetic_cars

A genetic algorithm car evolver in HTML5 canvas.

iq-tree

Efficient phylogenomic software by maximum likelihood

islr-tidymodels-labs

mf2_analyses

analyses for ModelFinder2 paper

minion_multiqc

multi-tool QC for minion data

minion_qc

Quality control for MinION sequencing data

mixturemodelhmm

Post-processes the output of phylogenetic mixture models using HMMs

ncov

Nextstrain build for novel coronavirus (nCoV)