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2019-domain_pnas

Software and data repository for PNAS paper 2019.

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.

alistat

amas

Calculate summary statistics and manipulate multiple sequence alignments

artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

assembly-stats

Assembly statistic visualisation

assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

augustus

Genome annotation with AUGUSTUS

avian-recomb

avian_indels_and_genome-size

bedtools

A powerful toolset for genome arithmetic.

bigramr

R package to calculate unigram and bigram frequencies of English words.

bioawk

BWK awk modified for biological data

bioinfo

Various bioinformatics tools

blast2bed

convert a blast output to a bed file

book

Compiled and pretty version of labs

breakdancer

SV detection from paired end reads mapping

brides

Characterizing the evolution of an original network X into an augmented network Y by counting the number of Breakthroughs, Roadblocks, Impasses, Detours, Equal paths and Shortcuts (BRIDES) in the network Y.

busco_phylogenomics

Utility script to construct species phylogenies using BUSCO results

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cactus

Official home of genome aligner based upon notion of Cactus graphs

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

cafexp

Version 5 of the CAFE phylogenetics software

cath-tools

Protein structure comparison tools such as SSAP and SNAP

cdhit

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

cnvnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

colibri-core

Colibri core is an NLP tool as well as a C++ and Python library for working with basic linguistic constructions such as n-grams and skipgrams (i.e patterns with one or more gaps, either of fixed or dynamic size) in a quick and memory-efficient way. At the core is the tool ``colibri-patternmodeller`` whi ch allows you to build, view, manipulate and query pattern models.

compositesearch

Composite gene families detection

course_rna-seq2015

crispr-grant

A cross-platform Graphical Analysis Tool for high-throughput CRISPR-based genome editing evaluation