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aylward_et_al_plos_one

aylwarddataviz

examples of data visualization, usually with 'omic or phylogenetic data

big616.github.io

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bioinfo-tutorials

Introductory tutorials in bioinformatics as applied to microbial genomics and metagenomics

bioinformatics_tutorials

tutorials

cshlii

dnds

fragment_recruitment

gene-characteristics

genomics_tutorial

Data for the Introduction to Gene Prediction Tutorial

gvdb

Giant Virus Database

hmm_introduction

homework for SYSB3036

hmm_question

hmm_tutorial

intro_to_metagenome_classification

introduction to using kraken2 and recentrifuge to classify metagenomic reads against an NCBI database

lastp_aai

script for calculating pairwise amino acid identity (AAI) between protein files

markerfinder

scripts for predicting phylogenetic marker genes

markerfinder-euk

This is a variation on the regular markerfinder script that can recover the three different eukaryotic RNAP variants

mlst

Short python script designed to identify housekeeping genes in protein files, concatenate them, and create a MLST phylogeny

ncldv

Supplementary Material

ncldv_markersearch

A tool for identifying phylogenetic marker genes in Nucleocytoviricota (giant viruses) and generating concatenated alignments.

ortholog_identifier

Wrapper script for the tool proteinortho, which identified orthologs between multiple sequenced genomes. Used here for amino acid sequences.

orthologs_tutorial

pangenomics

Scripts and utilities for pangenomic/phylogenomic analysis of prokaryotic genomes. Scripts for the analysis of genomic features such as C-ARSC, N-ARSC, and intergenic spacer lengths are also included.

pangenomics_tutorial

phylogenetics_tutorial

pmg

This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.

pmg_phylogeny

Tool for multilocus phylogenetics using different marker gene sets

portalcasting

Support Package for Portal Predictions

py-metagenomics

Some python libs and scripts for metagenomic analyses