RECENT POSTS
biology
May 26, 2018
- Ariadne - Programs to compare protein sequences and profiles
- Artemis - DNA sequence viewer and annotation tool
- Avida - Auto-adaptive genetic system designed for ALife research
- Babel - Converts among various molecular file formats
- Bamtools - API and toolkit for handling BAM files
- Bcftools - Tools for manipulating next-generation sequencing data
- Bedtools - Toolset for genome set arithmetic such as intersect, union
- Biococoa - Bioinformatics framework
- Blat - Fast tool for local sequence similarity searches
- Bowtie - Ultrafast, memory-efficient short read aligner
- Bowtie2 - Ultrafast, memory-efficient short read aligner
- Bwa - Burrows-Wheeler sequence aligner
- Canu - Single molecule sequence assembler
- Cd-hit - Clustering and comparing protein or nucleotide sequences
- Cdbfasta - Fast indexing and retrieval of FASTA records from flat file databases
- Chemeq - Outputs LaTeX code for chemical reaction
- Clustalw - Multiple alignment program for DNA or proteins
- Consed - Graphical tool for editing Phrap assemblies
- Crux - Software toolkit for phylogenetic inference
- Ddocent - Bash pipeline for RAD sequencing
- Diamond - BLAST-compatible local sequence aligner
- Emboss - Collection of open source tools for genetic sequence analysis
- Fasta - Collection of programs for searching DNA and protein databases
- Fasta3 - Collection of programs for searching DNA and protein databases
- Fastahack - Utility for indexing and sequence extraction from FASTA files
- Fastdnaml - Faster DNAML, makes phylogenetic trees using maximum likelihood
- Fastool - Simple and quick FastQ and FastA tool for file reading and conversion
- Fastqc - Quality control tool for high throughput sequence data
- Fasttree - Approximately-maximum-likelihood phylogenetic trees from alignments
- Fastx-toolkit - CLI tools for Short-Reads FASTA/FASTQ files preprocessing
- Fluctuate - Program to fit population models
- Freebayes - Bayesian haplotype-based polymorphism discovery and genotyping
- Garlic - Molecular viewer, editor, and visualization program
- Gff2ps - Converts gff-formated genomic data-sets to PostScript
- Gmap - Genomic Mapping and Alignment Program for mRNA and EST Sequences
- Gperiodic - Displays a periodic table of the elements
- Grappa - Genome Rearrangements Analysis and Phylogeny Software
- Hmmer - Profile hidden Markov models for biological sequence analysis
- Htslib - C library for high-throughput sequencing data formats
- Hyphy - Hypothesis testing using Phylogenies
- Iolib - General purpose trace file (and Experiment File) reading interface
- Iqtree - Efficient phylogenomic software by maximum likelihood
- Jalview - Viewer and editor for multiple sequence alignments
- Jellyfish - Fast, memory-efficient counting of k-mers in DNA
- Kallisto - Quantify abundances of transcripts from RNA-Seq data
- Lagan - Efficient tools for large-scale multiple alignments of genomic DNA
- Lamarc - Package of programs for computing population parameters
- Libgtextutils - Gordon's text utilities
- Libsbml - API Library for Working with SBML File
- Linux-foldingathome - Distributed client for Protein Folding
- Mafft - Multiple alignment program for amino acid or nucleotide sequences
- Mapm3 - Constructs linkage maps of markers segregating in experimental crosses
- Migrate - Program to estimate population sizes and migration rates
- Molden - Display molecular orbitals and electron densities in 2D and 3D
- Mopac - Semi-empirical (MNDO, etc.) molecular orbital calculation
- Mrbayes - Bayesian inference of phylogeny
- Mummer - Modular system for rapid whole genome alignment
- Muscle - MUltiple Sequence Comparison by Log-Expectation
- Ncbi-blast+ - NCBI implementation of Basic Local Alignment Search Tool
- Ncbi-toolkit - NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
- Njplot - Phylogenetic tree drawing program
- P5-aceperl - Perl5 interface to the ACEDB genome database system
- P5-bio-asn1-entrezgene - Regular expression-based Perl Parser for NCBI Entrez Gene
- P5-bio-coordinate - Modules for working with biological coordinates
- P5-bio-das-lite - Perl extension for the DAS (HTTP+XML) Protocol
- P5-bio-das - Client-side library for Distributed Genome Annotation System
- P5-bio-featureio - Handler for FeatureIO
- P5-bio-gff3 - Fast low-level functions for parsing and formatting GFF3
- P5-bio-glite - Perl Interface to G-language
- P5-bio-graphics - Generate GD Images of BioSeq Objects
- P5-bio-magetab - Data model and utility API for the MAGE-TAB format
- P5-bio-nexus - Object-oriented Perl API for the NEXUS file format
- P5-bio-phylo - Phylogenetic analysis using Perl
- P5-bio-scf - Read and Update SCF Chromatographic Sequence Files
- P5-bioperl-run - Wrapper modules for common bioinformatics tools
- P5-bioperl - Collection of Perl modules for bioinformatics
- P5-trimgalore - Wrapper around Cutadapt and FastQC for adapter and quality trimming
- P5-transdecoder - Identify candidate coding regions within transcript sequences
- Paml - Phylogenetic Analysis by Maximum Likelihood (PAML)
- Pbbam - PacBio BAM C++ library, with SWIG bindings
- Pbcopper - Core C++ library for Pacific Biosciences tools
- Pbseqan - Pacific Biosciences patched and stripped down SeqAn
- Pear-merger - Memory-efficient and highly accurate paired-end read merger
- Phrap - Phrap is a program for assembling shotgun DNA sequence data
- Phred - Base calling and quality value assignment on DNA sequencing
- Phylip - Phylogeny Inference Package
- Phyml - Simple, fast, and accurate algorithm to estimate large phylogenies
- Plink - Whole genome association analysis toolset
- Plinkseq - Toolset for working with human genetic variation data
- Primer3 - Primer3 helps to choose primers for PCR reactions
- Protomol - OO, component based, framework for molecular dynamics (MD) simulations
- Psi88 - Plotting wavefunctions (molecular orbitals) in 3D
- Py-biom-format - Biological Observation Matrix (BIOM) Format Project
- Py-biopython - Collection of Python modules for bioinformatics
- Py-bx-python - Python module for reading, manipulating and writing genomic data sets
- Py-cutadapt - Finds and removes adapter sequences, primers, poly-A tails, etc
- Py-macs2 - Analysis of chromatin immunoprecipitation (ChIP) sequences
- Py-pysam - Python module for reading, manipulating and writing genomic data sets
- Pycogent - Toolkit for statistical analysis of biological sequences
- Pyfasta - Fast, memory-efficient, pythonic access to fasta sequence files
- Python-nexus - Generic nexus file format reader for python
- Rainbow - Efficient clustering and assembling of short reads, especially for RAD
- Recombine - Program to fit population models across sites
- Ruby-bio - Integrated environment for Bioinformatics written in Ruby
- Rubygem-bio - Integrated environment for Bioinformatics written in Ruby
- Samtools - Tools for manipulating next-generation sequencing data
- Seaview - Multiple DNA/protein sequence alignment editor
- Seqan-apps - Official bioinformatic applications based on the SeqAn library
- Seqan - C++ sequence analysis template library
- Seqan1 - C++ Sequence Analysis Library
- Seqio - Set of C functions which can read/write biological sequence files
- Seqtk - Tool for processing sequences in FASTA/FASTQ format
- Seqtools - Tools for visualising sequence alignments
- Sim4 - Algorithm for aligning expressed DNA with genomic sequences
- Slclust - Single-linkage clustering with Jaccard similarity
- Smithwaterman - Smith-waterman-gotoh alignment algorithm
- Ssaha - Very fast matching and alignment of DNA sequences
- Stacks - Software pipeline for building loci from short-read sequences
- Trnascan-se - Improved tool for transfer RNA detection
- T_coffee - Multiple DNA or protein sequence alignment package
- Tabixpp - C++ wrapper to tabix indexer
- Tinker - General purpose molecular modelling package
- Treepuzzle - Maximum likelihood phylogeny reconstruction using quartets
- Trimadap - Trim adapter sequences from Illumina data using heuristic rules
- Trimmomatic - Flexible read trimming tool for Illumina NGS data
- Ugene - Free, open-source, cross-platform bioinformatics toolkit
- Unanimity - Pacific Biosciences consensus library and applications
- Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
- Vcftools - Tools for working with VCF genomics files
- Velvet - Sequence assembler for very short reads
- Wise - Intelligent algorithms for DNA searches
- Xmolwt - Calculate atom weight and percent of each element for a given formula
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