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2016_fips_tutorials

Protein-coding Evolution and Detecting Natural Selection | Tutorials

aaf

alignment and assembly free

all-branch-paml

Automated pipeline for selection test with designated model sets on each and every branch of a tree.

ark-server-tools

Set of server tools used to manage ARK: Survival Evolved servers on Linux

barcoding

Lima - Demultiplex Barcoded PacBio Samples

bioianalysing-and-interpreting-genomics-datasets

bioperl-live

Core BioPerl 1.x code

cc-linear-mixed-models

Introduction to linear mixed models

corset

Software for clustering de novo assembled transcripts and counting overlapping reads

data_file

docker-install

Docker installation script

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

extract_promoters

Bash script for promoter sequences extraction

fatools

A Python library for performing DNA fragment-analysis

fustr

gaas

Will contain all development done by the GAAS (Genome Assembly Annotation Service).

genomer

Contains useful R functions for dealing with genomic data

gff3sort

GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools

hipyproject

hpcleap_dnds

Sliding window dN/dS vs. functional protein domain comparison tool. Given VectorBase gene id inputs it will aggregate various useful Bioinformatics information available, then allow the user to compare selective pressures acting along the protein sequence vs. an overlay of functional protein domain annotations.

intro_to_r

isoseq_sa3nup

Documentation and Developers Code Base for Iso-Seq SMRTAnalysis 3.x and beyond

life113

Resources associated with LIFE113 Quantitative Biology I module. School of Life Sciences, University of Liverpool

lwp-protocol-https

Provide https support for LWP::UserAgent

maftools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

marvel

The MARVEL assembler

mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

oneliners

Useful bash one-liners for bioinformatics.