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afterphylo

Perl script for manipulating trees after phylogenetic reconstruction

american-gut-web

The website for the American Gut Project participant portal

beforephylo

Perl script for manipulating multiple sequence alignments for phylogenetic reconstruction

binarena

binarena-manuscript

bio598-2021

BIO/MIC 494/598 Microbiome Data Science

bioconda-recipes

Conda recipes for the bioconda channel.

biom-format

The Biological Observation Matrix (BIOM) Format Project

calour

exploratory and interactive microbiome analyses based on heatmaps

conda-recipes

conda recipes for bioinformatic tools like blast+, infernal, etc.

deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.

dsfdr

descrete False Discovery Rate method

emp

Data, code and analysis results for the Earth Microbiome Project.

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

empress

A very fast and scalable phylogenetic visualization viewer

ezcalour

GUI for Calour functions

genome-subsampler

genordi

Match read alignments and annotated genes in an ordinal scale on genome.

gneiss

compositional data analysis and visualization toolbox

hgtector

Genome-wide prediction of horizontal gene transfer events based on Blast hit distribution statistics

horizomer

Workflow for detecting genome-wide horizontal gene transfers

labadmin

Administration website for the Knight Lab

labman

lab manager for plate maps and sequence flows

metadata-ideas

micronota

annotation pipeline for microbial genomes and metagenomes

microprot

structural annotation pipeline for microbial genomes and metagenomes

oecophylla

shotgun pipeline

phylomizer

PhylomeDB automated pipeline for reconstructing high-quality phylogenetic tree

q2-chemistree

Hierarchical orderings for mass spectrometry data

q2-fragment-insertion

QIIME2 plugin for fragment insertion