| maq |
Mapping and Assembly with Qualities, mapping NGS reads to reference genomes |
| embassy |
A meta-package for installing all EMBASSY packages (EMBOSS add-ons) |
| tree-puzzle |
Maximum likelihood analysis for nucleotide, amino acid, and two-state data |
| embassy-phylipnew |
EMBOSS integrated version of The Phylogeny Inference Package |
| aaindex |
Amino acid indices and similarity matrices |
| emboss |
The European Molecular Biology Open Software Suite - A sequence analysis package |
| maqview |
GUI for sci-biology/maq, a short read mapping assembler |
| vienna-rna |
RNA secondary structure prediction and comparison |
| cd-hit |
Clustering Database at High Identity with Tolerance |
| sim4 |
A program to align cDNA and genomic DNA |
| ApE |
A Plasmid Editor |
| blat |
The BLAST-Like Alignment Tool, a fast genomic sequence aligner |
| diya |
Do It Yourself Annotation, tools & libraries for sequence assembly & annotation |
| biosql |
A generic bioinformatics relational database model |
| bowtie |
Popular short read aligner for Next-generation sequencing data |
| bwa |
Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner |
| dialign2 |
Multiple sequence alignment |
| elph |
Estimated Locations of Pattern Hits - Motif finder program |
| embassy-cbstools |
EMBOSS integrated version of Applications from the CBS group |
| embassy-clustalomega |
EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment |
| embassy-esim4 |
EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA |
| embassy-hmmer |
EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs |
| embassy-iprscan |
EMBOSS integrated version of InterProScan motif detection add-on package |
| embassy-meme |
EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation |
| embassy-mse |
EMBOSS integrated version of MSE - Multiple Sequence Screen Editor |
| gibbs |
Identify motifs, conserved regions, in DNA or protein sequences |
| glimmer |
An HMM-based microbial gene finding system from TIGR |
| glimmerhmm |
A eukaryotic gene finding system from TIGR |
| finchtv |
Graphical viewer for chromatogram files |
| foldingathome |
Folding@Home is a distributed computing project for protein folding |
| gatk |
The Genome Analysis Toolkit |
| libgtextutils |
Gordon Text utils Library |
| mafft |
Multiple sequence alignments using a variety of algorithms |
| gmap |
A Genomic Mapping and Alignment Program for mRNA and EST Sequences |
| hmmer |
Sequence analysis using profile hidden Markov models |
| iedera |
A subset seed design tool for DNA sequence alignment |
| infernal |
Inference of RNA alignments |
| iqpnni |
Important Quartet Puzzling and NNI Operation |
| lagan |
The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA |
| mcl |
A Markov Cluster Algorithm implementation |
| meme |
The MEME/MAST system - Motif discovery and search |
| mira |
Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina |
| mosaik |
A reference-guided aligner for next-generation sequencing technologies |
| mothur |
A suite of algorithms for ecological bioinformatics |
| muscle |
Multiple sequence comparison by log-expectation |
| ncbi-tools |
Development toolkit and applications for computational biology, including BLAST |
| newick-utils |
Tools for processing phylogenetic trees |
| njplot |
A phylogenetic tree drawing program which supports tree rooting |
| pals |
Pairwise Aligner for Long Sequences |
| paml |
Phylogenetic Analysis by Maximum Likelihood |
| phrap |
Shotgun assembly and alignment utilities |
| phred |
A base caller for Sanger DNA sequencing |
| phylip |
The PHYLogeny Inference Package |
| phyml |
Estimation of large phylogenies by maximum likelihood |
| picard |
Java-based command-line utilities that manipulate SAM files |
| piler |
Analysis of repetitive DNA found in genome sequences |
| pilercr |
Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) |
| plink |
Whole genome association analysis toolset |
| poa |
Fast multiple sequence alignments using partial-order graphs |
| prank |
Probabilistic Alignment Kit |
| profphd |
Secondary structure and solvent accessibility predictor |
| primer3 |
Primer Design for PCR reactions |
| prints |
A protein motif fingerprint database |
| probcons |
Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences |
| prodigal |
Prokaryotic Dynamic Programming Genefinding Algorithm |
| prosite |
A protein families and domains database |
| seaview |
A graphical multiple sequence alignment editor |
| repeatmasker |
Screen DNA sequences for interspersed repeats and low complexity DNA |
| rmblast |
RepeatMasker compatible version of NCBI BLAST+ |
| rnaview |
Generates 2D displays of RNA/DNA secondary structures with tertiary interactions |
| seqan |
C++ Sequence Analysis Library |
| shrimp |
SHort Read Mapping Package |
| sibsim4 |
A rewrite and improvement upon sim4, a DNA-mRNA aligner |
| treeviewx |
A phylogenetic tree viewer |
| uchime |
Fast, accurate chimera detection |
| unafold |
Unified Nucleic Acid Folding and hybridization package |
| update-blastdb |
update_blastdb.pl for local blast db maintainance |
| vcftools |
Tools for working with VCF (Variant Call Format) files |
| velvet |
A sequence assembler for very short reads |
| GBrowse |
Generic Model Organism Database Project - The Generic Genome Browser |
| HTSeq |
Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files |
| bedtools |
Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats |
| embassy-domainatrix |
EMBOSS integrated version of Protein domain analysis add-on package |
| embassy-domalign |
EMBOSS integrated version of Protein domain alignment add-on package |
| embassy-domsearch |
EMBOSS integrated version of Protein domain search add-on package |
| embassy-emnu |
EMBOSS integrated version of Simple menu of EMBOSS applications |
| samtools |
Utilities for analysing and manipulating the SAM/BAM alignment formats |
| stride |
Protein secondary structure assignment from atomic coordinates |
| ucsc-genome-browser |
The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath |
| bioperl-network |
Perl tools for bioinformatics - Analysis of protein-protein interaction networks |
| bioperl-run |
Perl wrapper modules for key bioinformatics applications |
| bioperl |
Perl tools for bioinformatics - Core modules |
| biopython |
Python modules for computational molecular biology |
| embassy-signature |
EMBOSS integrated version of Protein signature add-on package |
| embassy-structure |
EMBOSS integrated version of Protein structure add-on package |
| embassy-topo |
EMBOSS integrated version of Transmembrane protein display |
| embassy-vienna |
EMBOSS integrated version of Vienna RNA package - RNA folding |
| kalign |
Global and progressive multiple sequence alignment |
| kallisto |
Near-optimal RNA-Seq quantification |
| STAR |
STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays |
| abyss |
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
| amap |
Protein multiple-alignment-based sequence annealing |
| amos |
A Modular, Open-Source whole genome assembler |
| augustus |
Eukaryotic gene predictor |
| bamtools |
A programmer's API and an end-user's toolkit for handling BAM files |
| bcftools |
Utilities for variant calling and manipulating VCF and BCF files |
| bfast |
Blat-like Fast Accurate Search Tool |
| biogrep |
Multithreaded tool for matching large sets of patterns against biosequence DBs |
| biopandas |
Molecular Structures in Pandas DataFrames |
| bioperl-db |
Perl tools for bioinformatics - Perl API that accesses the BioSQL schema |
| clustal-omega |
Scalable multiple alignment of protein sequences |
| clustalw-mpi |
An MPI implemention of the ClustalW general purpose multiple alignment algorithm |
| clustalw |
General purpose multiple alignment program for DNA and proteins |
| clustalx |
Graphical interface for the ClustalW multiple alignment program |
| consed |
A genome sequence finishing program |
| cutg |
Codon usage tables calculated from GenBank |
| dialign-tx |
Greedy and progressive approaches for segment-based multiple sequence alignment |
| eugene |
Prokaryotic and Eukaryotic gene predictor |
| exonerate |
Generic tool for pairwise sequence comparison |
| express |
Streaming RNA-Seq Analysis |
| fasta |
FASTA is a DNA and Protein sequence alignment software package |
| fasttree |
Fast inference of approximately-maximum-likelihood phylogenetic trees |
| fastx_toolkit |
Tools for Short Read FASTA/FASTQ file processing |
| mrbayes |
Bayesian Inference of Phylogeny |
| mummer |
A rapid whole genome aligner |
| psipred |
Protein Secondary Structure Prediction |
| pysam |
Python interface for the SAM/BAM sequence alignment and mapping format |
| qrna |
Prototype ncRNA genefinder |
| raxml |
Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees |
| rebase |
A restriction enzyme database |
| recon |
Automated de novo identification of repeat families from genomic sequences |
| repeatmasker-libraries |
A special version of RepBase used by RepeatMasker |
| t-coffee |
A multiple sequence alignment package |
| transfac |
A database of eucaryotic transcription factors |
| trf |
Tandem Repeats Finder |
| trnascan-se |
tRNA detection in large-scale genome sequences |
| wgs-assembler |
The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG |
| wise |
Intelligent algorithms for DNA searches |
| yass |
Genomic similarity search with multiple transition constrained spaced seeds |
Packages