The sci-biology category contains software that can be used in biological and related scientific environments.
| aaindex | Amino acid indices and similarity matrices |
|---|---|
| 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 |
| ApE | A Plasmid Editor |
| 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 |
| bedtools | Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats |
| 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 | Perl tools for bioinformatics - Core modules |
| bioperl-db | Perl tools for bioinformatics - Perl API that accesses the BioSQL schema |
| bioperl-network | Perl tools for bioinformatics - Analysis of protein-protein interaction networks |
| bioperl-run | Perl wrapper modules for key bioinformatics applications |
| biopython | Python modules for computational molecular biology |
| bioruby | An integrated environment for bioinformatics using the Ruby language |
| biosql | A generic bioinformatics relational database model |
| blat | The BLAST-Like Alignment Tool, a fast genomic sequence aligner |
| bowtie | Popular short read aligner for Next-generation sequencing data |
| bwa | Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner |
| cd-hit | Clustering Database at High Identity with Tolerance |
| clustal-omega | Scalable multiple alignment of protein sequences |
| clustalw | General purpose multiple alignment program for DNA and proteins |
| clustalw-mpi | An MPI implemention of the ClustalW general purpose multiple alignment algorithm |
| 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 |
| dialign2 | Multiple sequence alignment |
| diya | Do It Yourself Annotation, tools & libraries for sequence assembly & annotation |
| elph | Estimated Locations of Pattern Hits - Motif finder program |
| embassy | A meta-package for installing all EMBASSY packages (EMBOSS add-ons) |
| embassy-cbstools | EMBOSS integrated version of Applications from the CBS group |
| embassy-clustalomega | EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment |
| 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 |
| 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 |
| embassy-phylipnew | EMBOSS integrated version of The Phylogeny Inference Package |
| 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 |
| emboss | The European Molecular Biology Open Software Suite - A sequence analysis package |
| 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 |
| finchtv | Graphical viewer for chromatogram files |
| foldingathome | Folding@Home is a distributed computing project for protein folding |
| gatk | The Genome Analysis Toolkit |
| GBrowse | Generic Model Organism Database Project - The Generic Genome Browser |
| 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 |
| gmap | A Genomic Mapping and Alignment Program for mRNA and EST Sequences |
| hmmer | Sequence analysis using profile hidden Markov models |
| HTSeq | Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files |
| iedera | A subset seed design tool for DNA sequence alignment |
| infernal | Inference of RNA alignments |
| iqpnni | Important Quartet Puzzling and NNI Operation |
| kalign | Global and progressive multiple sequence alignment |
| kallisto | Near-optimal RNA-Seq quantification |
| lagan | The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA |
| last | Genome-scale comparison of biological sequences |
| libgtextutils | Gordon Text utils Library |
| mafft | Multiple sequence alignments using a variety of algorithms |
| maq | Mapping and Assembly with Qualities, mapping NGS reads to reference genomes |
| maqview | GUI for sci-biology/maq, a short read mapping assembler |
| 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 |
| mrbayes | Bayesian Inference of Phylogeny |
| mummer | A rapid whole genome aligner |
| 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 |
| 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 |
| profphd | Secondary structure and solvent accessibility predictor |
| prosite | A protein families and domains database |
| 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 | Screen DNA sequences for interspersed repeats and low complexity DNA |
| repeatmasker-libraries | A special version of RepBase used by RepeatMasker |
| rmblast | RepeatMasker compatible version of NCBI BLAST+ |
| rnaview | Generates 2D displays of RNA/DNA secondary structures with tertiary interactions |
| samtools | Utilities for analysing and manipulating the SAM/BAM alignment formats |
| seaview | A graphical multiple sequence alignment editor |
| seqan | C++ Sequence Analysis Library |
| shrimp | SHort Read Mapping Package |
| sibsim4 | A rewrite and improvement upon sim4, a DNA-mRNA aligner |
| sim4 | A program to align cDNA and genomic DNA |
| STAR | STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays |
| stride | Protein secondary structure assignment from atomic coordinates |
| t-coffee | A multiple sequence alignment package |
| tophat | Python-based splice junction mapper for RNA-Seq reads using bowtie2 |
| transfac | A database of eucaryotic transcription factors |
| tree-puzzle | Maximum likelihood analysis for nucleotide, amino acid, and two-state data |
| treeviewx | A phylogenetic tree viewer |
| trf | Tandem Repeats Finder |
| trnascan-se | tRNA detection in large-scale genome sequences |
| uchime | Fast, accurate chimera detection |
| ucsc-genome-browser | The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath |
| 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 |
| vienna-rna | RNA secondary structure prediction and comparison |
| 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 |