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2kplus2

2kplus2 bubbles detection

2matrix

A utility for merging and translating phylogenetic datasets

abc

Allele-specific Binding from Chip-seq

abra

Assembly Based ReAligner

abyss

de novo sequence assembler

ace

ACE: Accurate Correction of Errors

aci

Atom Column Indexing

acme

This repository contains open-source C++ code for reconstructing membranes from time-lapse confocal/2-photon image data. Please refer to the webpage below for detailed instructions, precompiled binaries, and sample data for testing the code.

acquire

Baylor College of Medicine Biobanking Software

adapt_mix

afcluster

alignment free clustering utility

affylumcna

Copy Number Alterations: Preprocessing, integration, and analysis of Affymetrix and Illumina data

affypipe

an open-source pipeline for Affymetrix Axiom genotyping workflow on livestock species

agplus

a rapid and flexible tool for aggregation plots

aksmooth

Ajusted local kernel smoothing for bisulfite sequencing data

al3c

al3c

aligngraph

Algorithm for secondary de novo genome assembly guided by closely related references

aliview

Software for aligning viewing and editing dna/aminiacid sequences, intuitive, fast and leightweight

andi

annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts.

ap11_samifier

Mascot (peptide) search results converted into SAM format

arch-galaxy

Provides PhyloTastic services in the Galaxy environment. Implemented in Perl.

arch-ne

ARCH vascular Network Editor

architastic

Controllers for phylotastic components

arioc

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

arraymaker

Creates transposed PED files of SNP genotypes at chosen loci from BAM files of mammalian whole genome sequence data

arts

Tools for study randomization

assign

ASSIGN is an R package for adaptive profiling of genomic signatures

astral

Accurate Species TRee ALgorithm

atma