guyleonard/genomics_adventure

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guyleonard/genomics_adventure

guyleonard

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Workshop on Genomics - Genomics Adventure

get_jgi_genomes

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

jsPhyloSVG

taxdump_edit

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

orthomcl_tools

A couple of tools I find indispensable for post orthomcl down-stream analysis.

gene_prediction_pipeline

Gene Prediction using MAKER, CEGMA, SNAP, GENEMARK & AUGUSTUS

sagawe

⚪ ➡️ 🔍 ℹ️ A suggested workflow, and accompanying scripts, to assemble Single Amplified Genomes (SAGs) from MDA derived Hi/MiSeq (Overlapped) Paired-End Illumina Libraries.

busco_hmms_for_anvio

Making BUSCO HMMs useable in Anvi'o.

refgen

A time-saving tool to change the 'defline' of FASTA files for a range of phylogenetic programs e.g. ClustalX, MrBayes, PhyML

get_ensembl_genomes

A quick and easy way to download the genomes/predicted proteins of taxa available from ENSEMBL Genomes

orthagogue

Automatically exported from code.google.com/p/orthagogue

random_scripts

A collection of random scripts I have made over the years, barely any documentation though. Enjoy, be careful!

fdfBLAST

evomics_2017

Creating the AMI for the evomics.org Workshops

genome_crossovers

Which genomes are where in the big DBs?

blastocladiella

The genome of Blastocladiella emersonii

evomics_2019

Creating the Virtual Machine (AMI) for the evomics.org Workshops

treenamer

Reddit-Perl-API

A simple Perl API to query Reddit

marine_fungi

Accompanying files for Identification of 71 marine fungal lineages using diversity tag sequencing 2015, In prep.

taxa_autocorrect

A tool to 'automagically' italicise taxon names, compiled from 839 taxa sampled from NCBI, DOE JGI and BROAD. Currently MS Word only

easyRAx

The script aims to make execution of RAxML a little easier by use of simple command-line menus and some user input.

orchard

🌱 📋 ➡️ 🎱 ➡️ 🌴 🌲 🌳 - A quick phylogenetic tree building pipeline!

hgt_oomycetes

Horizontal gene transfer (HGT) or lateral gene transfer (LGT) involves the transmission of genetic material between distinct evolutionary lineages and can be an important source of biological innovation. For instance, the acquisition of foreign genes can allow recipient organisms to adapt to new lifestyles or to exploit a novel ecological niche, such as a host environment. HGT has long been recognised as an important factor contributing to the evolution of prokaryotic lineages especially in connection to the evolution of pathogencity [1,2]. However, it is becoming increasingly apparent that HGT has also played a role in the evolution of pathogenic traits in eukaryotes [3,4]. Here, we consider how HGT has contributed to genome evolution in the oomycetes.