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