Fasta

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db... Platforms: *nix

Fasta is a small utility what was designed to let you quickly run frequently used programs, documents, etc. You can access your favorite applications using its name or aliase. Just press Hot Keys to bring up the main window, type name of application or URL and press Enter. Platforms: Windows

Sirocco AFastAMaker is a simple and handy tool built using Java that allows you to create Fasta files. The Fasta files built using this software can then be used with other tools. Now you can create the Fasta files you need in no time at all. Platforms: Windows

Pythonic access to fasta sequence files pyfasta is a library that offers Pythonic access to fasta sequence files. Usage: .. sourcecode:: python >>> from pyfasta import Fasta >>> f = Fasta('tests/data/three_chrs.fasta') >>> sorted(f.keys()) ['chr1', 'chr2', 'chr3'] >>> f['chr1']... Platforms: *nix

ChromatoGate is a lightweight application that was designed in order to help you easily generate consensus sequences and preliminary fasta files to be used for alignment. ChromatoGate can also be useful for detecting ambiguous characters in an input alignment and the respective chromatogram... Platforms: Windows

InFASTA - cross-platform software for FASTA file manipulation Platforms: Windows, Mac, Linux

The conventional tree view is a natural way to represent a dendrogram but is only usable for very small trees.Using the interactive power of computers we can build a more compact view. Leaves are represented as points on a grid. Boxes are drawn round the points to represent the hierarchy. It is... Platforms: PHP

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of... Platforms: Mac

BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done. Platforms: *nix

AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20... Platforms: *nix

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #... Platforms: *nix

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =... Platforms: *nix

BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.... Platforms: *nix

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research. They are licenced under the LGPL. he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction... Platforms: *nix

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create... Platforms: *nix

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #... Platforms: *nix

Bio::SeqIO::fastq is a fastq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::SeqIO class. This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases. Fastq is a file format used frequently at... Platforms: *nix

4Peaks is a program that helps molecular biologists to visualize and edit their DNA sequence files. At last there is a decent solution for analyzing trace files on the Mac OS X platform, taking another step away from slow and non-native programs from the Mac OS 9 period. Also, 4Peaks supports... Platforms: Mac

CLC Free Workbench is the foundation for all bioinformatics workbenches from CLC bio. This software package is a community edition, available for download free of charge.The workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management,... Platforms: Mac

MacVector... Researchers who want a simple but comprehensive desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence... Platforms: Mac