Description of Genome Annotation Procedures

GEN220 course, Fall 2015 edition

simulation for manuscript "Coevolution leaves a weak signal on ecological networks" (DOI: 10.1002/ecs2.1798) to generate ecological networks

Guiding principles of the Ponisio lab

RAxML Next Generation: faster, easier-to-use and more flexible

phylogenetics tools for linux (and other mostly posix compliant) computers

A LaTeX template / tutorial

A guide to learn bash

Provides a local database of all completed genomes for Bacteria and Archaea from NCBI

Microbiome tools and resources for Stajichlab projects

Scripts and data for a manuscript entitled "Contribution of North American endophytic and endolichenic fungi to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota)"

Accurate sample inference from amplicon data with single nucleotide resolution

An analysis and visualization platform for 'omics data

Interactive assembly and analysis of RAD-seq data sets

MEGAN Community Edition

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

Gordon's Text utils Library

FASTA/FASTQ pre-processing programs

A robust and fast clustering method for amplicon-based studies

The fundamental package for scientific computing with Python.

Cutadapt removes adapter sequences from sequencing reads

The hackable text editor

Official git repository for Biopython (originally converted from CVS)

The BioPerl Web site: http://bioperl.org

Core BioPerl 1.x code

Postprocessing gadgets for output generated by RevBayes

Compilation of tutorials for RevBayes