wwood Goto Github PK

abisko-stuff

Abisko project-specific R scripts (and maybe more later)

ace2sam

(fork) Converts an ACE alignment to a SAM file

ale

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

amplicon_encyclopaedia

TODO: one-line summary of your gem

annotatem

annotate my genome

ape

Patched version of the ape R library to run cophenetic on larger trees

apiloc

A curated database of protein sub-cellular localisation in apicomplexan parasites

apilocserver

The web interface behind the ApiLoc server

argparse-manpage-birdtools

Automatically build man-pages for your Python project

array_pair

random useful methods for working with Ruby arrays, hashes and objects

aviary

A snakemake pipeline for binning metagenomic assemblies

aws-genomics-workflows

Genomics Workflows on AWS

bacterial_dating_aerobic_predictor

Prediction of aerobicity in extant and ancient genomes

bamm

BamM

bbbin

A collection of working and non-working bioinformatics scripts

ben_bioinformatics

A collection of random bioinformatic rails plugin

beta_diversity_squares

visualise ecological beta diversity

binning_refiner

bio-kseq

Ruby inferface for kseq.h by Heng Li for fast FASTA/Q reading

bioconda-recipes

Conda recipes for the bioconda channel.

biogems.info

Tools for keeping track of biogems

biolib

Python package for common tasks in bioinformatic.

biopython

Official git repository for Biopython (converted from CVS)

bioruby

bioruby

bioruby-aliphatic_index

TODO: one-line summary of your gem

bioruby-cigar

A parser for CIGAR format alignments

bioruby-cnls_screenscraper

a bioruby plugin for interaction with the cNLS (classical Nuclear Localisation Signal) predictor

bioruby-cog_categories

API to Clusters of Orthologous Groups of proteins (COGs) functional categories

bioruby-commandeer

A dead simple method of running shell commands from within Ruby

bioruby-emboss_six_frame_nucleotide_sequences

a method to get the nucleotide sequence of translations done by the EMBOSS bioinformatics package program transeq