sci-biology packages

147 packages - The sci-biology category contains software that can be used in biological and related scientific environments.

sci-biology / ApE : A Plasmid Editor

sci-biology / GBrowse : Generic Model Organism Database Project - The Generic Genome Browser

sci-biology / HTSeq : Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files

sci-biology / STAR : STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays

sci-biology / aaindex : Amino acid indices and similarity matrices

sci-biology / abyss : Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

sci-biology / allpathslg : De novo assembly of whole-genome shotgun microreads

sci-biology / amap : Protein multiple-alignment-based sequence annealing

sci-biology / amos : A Modular, Open-Source whole genome assembler

sci-biology / ariadne : Protein sequences and profiles comparison

sci-biology / augustus : Eukaryotic gene predictor

sci-biology / bamtools : A programmer's API and an end-user's toolkit for handling BAM files

sci-biology / bcftools : Utilities for variant calling and manipulating VCF and BCF files

sci-biology / bedtools : Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats

sci-biology / bfast : Blat-like Fast Accurate Search Tool

sci-biology / biogrep : Multithreaded tool for matching large sets of patterns against biosequence DBs

sci-biology / biopandas : Molecular Structures in Pandas DataFrames

sci-biology / bioperl : Perl tools for bioinformatics - Core modules

sci-biology / bioperl-db : Perl tools for bioinformatics - Perl API that accesses the BioSQL schema

sci-biology / bioperl-network : Perl tools for bioinformatics - Analysis of protein-protein interaction networks

sci-biology / bioperl-run : Perl wrapper modules for key bioinformatics applications

sci-biology / biopython : Python modules for computational molecular biology

sci-biology / bioruby : An integrated environment for bioinformatics using the Ruby language

sci-biology / biosql : A generic bioinformatics relational database model

sci-biology / blat : The BLAST-Like Alignment Tool, a fast genomic sequence aligner

sci-biology / bowtie : Popular short read aligner for Next-generation sequencing data

sci-biology / bwa : Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner

sci-biology / cd-hit : Clustering Database at High Identity with Tolerance

sci-biology / clustal-omega : Scalable multiple alignment of protein sequences

sci-biology / clustalw : General purpose multiple alignment program for DNA and proteins

sci-biology / clustalw-mpi : An MPI implemention of the ClustalW general purpose multiple alignment algorithm

sci-biology / clustalx : Graphical interface for the ClustalW multiple alignment program

sci-biology / consed : A genome sequence finishing program

sci-biology / cutg : Codon usage tables calculated from GenBank

sci-biology / dialign-tx : Greedy and progressive approaches for segment-based multiple sequence alignment

sci-biology / dialign2 : Multiple sequence alignment

sci-biology / diya : Do It Yourself Annotation, tools & libraries for sequence assembly & annotation

sci-biology / elph : Estimated Locations of Pattern Hits - Motif finder program

sci-biology / embassy : A meta-package for installing all EMBASSY packages (EMBOSS add-ons)

sci-biology / embassy-cbstools : EMBOSS integrated version of Applications from the CBS group

sci-biology / embassy-clustalomega : EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment

sci-biology / embassy-domainatrix : EMBOSS integrated version of Protein domain analysis add-on package

sci-biology / embassy-domalign : EMBOSS integrated version of Protein domain alignment add-on package

sci-biology / embassy-domsearch : EMBOSS integrated version of Protein domain search add-on package

sci-biology / embassy-emnu : EMBOSS integrated version of Simple menu of EMBOSS applications

sci-biology / embassy-esim4 : EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA

sci-biology / embassy-hmmer : EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs

sci-biology / embassy-iprscan : EMBOSS integrated version of InterProScan motif detection add-on package

sci-biology / embassy-meme : EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation

sci-biology / embassy-mse : EMBOSS integrated version of MSE - Multiple Sequence Screen Editor

sci-biology / embassy-phylipnew : EMBOSS integrated version of The Phylogeny Inference Package

sci-biology / embassy-signature : EMBOSS integrated version of Protein signature add-on package

sci-biology / embassy-structure : EMBOSS integrated version of Protein structure add-on package

sci-biology / embassy-topo : EMBOSS integrated version of Transmembrane protein display

sci-biology / embassy-vienna : EMBOSS integrated version of Vienna RNA package - RNA folding

sci-biology / emboss : The European Molecular Biology Open Software Suite - A sequence analysis package

sci-biology / eugene : Prokaryotic and Eukaryotic gene predictor

sci-biology / exonerate : Generic tool for pairwise sequence comparison

sci-biology / express : Streaming RNA-Seq Analysis

sci-biology / fasta : FASTA is a DNA and Protein sequence alignment software package

sci-biology / fasttree : Fast inference of approximately-maximum-likelihood phylogenetic trees

sci-biology / fastx_toolkit : Tools for Short Read FASTA/FASTQ file processing

sci-biology / finchtv : Graphical viewer for chromatogram files

sci-biology / foldingathome : Folding@Home is a distributed computing project for protein folding

sci-biology / gatk : The Genome Analysis Toolkit

sci-biology / gibbs : Identify motifs, conserved regions, in DNA or protein sequences

sci-biology / glimmer : An HMM-based microbial gene finding system from TIGR

sci-biology / glimmerhmm : A eukaryotic gene finding system from TIGR

sci-biology / gmap : A Genomic Mapping and Alignment Program for mRNA and EST Sequences

sci-biology / goby : A DNA sequencing data management framework

sci-biology / goby-cpp : A DNA sequencing data management framework - C/C++ API

sci-biology / hmmer : Sequence analysis using profile hidden Markov models

sci-biology / iedera : A subset seed design tool for DNA sequence alignment

sci-biology / infernal : Inference of RNA alignments

sci-biology / iqpnni : Important Quartet Puzzling and NNI Operation

sci-biology / kalign : Global and progressive multiple sequence alignment

sci-biology / kallisto : Near-optimal RNA-Seq quantification

sci-biology / lagan : The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA

sci-biology / last : Genome-scale comparison of biological sequences

sci-biology / libgtextutils : Gordon Text utils Library

sci-biology / mafft : Multiple sequence alignments using a variety of algorithms

sci-biology / maq : Mapping and Assembly with Qualities, mapping NGS reads to reference genomes

sci-biology / maqview : GUI for sci-biology/maq, a short read mapping assembler

sci-biology / mcl : A Markov Cluster Algorithm implementation

sci-biology / meme : The MEME/MAST system - Motif discovery and search

sci-biology / mira : Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina

sci-biology / mosaik : A reference-guided aligner for next-generation sequencing technologies

sci-biology / mothur : A suite of algorithms for ecological bioinformatics

sci-biology / mrbayes : Bayesian Inference of Phylogeny

sci-biology / mummer : A rapid whole genome aligner

sci-biology / muscle : Multiple sequence comparison by log-expectation

sci-biology / ncbi-tools : Development toolkit and applications for computational biology, including BLAST

sci-biology / newick-utils : Tools for processing phylogenetic trees

sci-biology / njplot : A phylogenetic tree drawing program which supports tree rooting

sci-biology / pals : Pairwise Aligner for Long Sequences

sci-biology / paml : Phylogenetic Analysis by Maximum Likelihood

sci-biology / phrap : Shotgun assembly and alignment utilities

sci-biology / phred : A base caller for Sanger DNA sequencing

sci-biology / phylip : The PHYLogeny Inference Package

sci-biology / phyml : Estimation of large phylogenies by maximum likelihood

sci-biology / picard : Java-based command-line utilities that manipulate SAM files

sci-biology / piler : Analysis of repetitive DNA found in genome sequences

sci-biology / pilercr : Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)

sci-biology / plink : Whole genome association analysis toolset

sci-biology / poa : Fast multiple sequence alignments using partial-order graphs

sci-biology / prank : Probabilistic Alignment Kit

sci-biology / primer3 : Primer Design for PCR reactions

sci-biology / prints : A protein motif fingerprint database

sci-biology / probcons : Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

sci-biology / prodigal : Prokaryotic Dynamic Programming Genefinding Algorithm

sci-biology / profphd : Secondary structure and solvent accessibility predictor

sci-biology / prosite : A protein families and domains database

sci-biology / psipred : Protein Secondary Structure Prediction

sci-biology / pysam : Python interface for the SAM/BAM sequence alignment and mapping format

sci-biology / qrna : Prototype ncRNA genefinder

sci-biology / raxml : Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees

sci-biology / rebase : A restriction enzyme database

sci-biology / recon : Automated de novo identification of repeat families from genomic sequences

sci-biology / repeatmasker : Screen DNA sequences for interspersed repeats and low complexity DNA

sci-biology / repeatmasker-libraries : A special version of RepBase used by RepeatMasker

sci-biology / rmblast : RepeatMasker compatible version of NCBI BLAST+

sci-biology / rnaview : Generates 2D displays of RNA/DNA secondary structures with tertiary interactions

sci-biology / samtools : Utilities for analysing and manipulating the SAM/BAM alignment formats

sci-biology / seaview : A graphical multiple sequence alignment editor

sci-biology / seqan : C++ Sequence Analysis Library

sci-biology / shrimp : SHort Read Mapping Package

sci-biology / sibsim4 : A rewrite and improvement upon sim4, a DNA-mRNA aligner

sci-biology / sim4 : A program to align cDNA and genomic DNA

sci-biology / stride : Protein secondary structure assignment from atomic coordinates

sci-biology / t-coffee : A multiple sequence alignment package

sci-biology / tophat : Python-based splice junction mapper for RNA-Seq reads using bowtie2

sci-biology / transfac : A database of eucaryotic transcription factors

sci-biology / tree-puzzle : Maximum likelihood analysis for nucleotide, amino acid, and two-state data

sci-biology / treeviewx : A phylogenetic tree viewer

sci-biology / trf : Tandem Repeats Finder

sci-biology / trnascan-se : tRNA detection in large-scale genome sequences

sci-biology / uchime : Fast, accurate chimera detection

sci-biology / ucsc-genome-browser : The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath

sci-biology / unafold : Unified Nucleic Acid Folding and hybridization package

sci-biology / update-blastdb : update_blastdb.pl for local blast db maintainance

sci-biology / vaal : Algorithm for detecting SNPs, indels, and other polymorphisms

sci-biology / vcftools : Tools for working with VCF (Variant Call Format) files

sci-biology / velvet : A sequence assembler for very short reads

sci-biology / vienna-rna : RNA secondary structure prediction and comparison

sci-biology / wgs-assembler : The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG

sci-biology / wise : Intelligent algorithms for DNA searches

sci-biology / yass : Genomic similarity search with multiple transition constrained spaced seeds