Alignments
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
License: Freeware | Size: 348.16 KB | Download (96): AlignAid Download |
Cylindrical BLAST Viewer is a small, easy to use application specially designed to offer users a 3D viewer that arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display.
Basically this tool arranges the alignments in a cylinder, which spins past the eye...
Platforms: Windows
License: Freeware | Download (489): Cylindrical BLAST Viewer Download |
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
License: Freeware | Size: 82.94 KB | Download (101): Bio::Tools::Run::PiseApplication::fasta Download |
GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
It is free software under GPLv2+.
Requested Features:
- Import of Vector NTI...
Platforms: Mac
License: Freeware | Size: 3.7 MB | Download (600): GENtle for Mac OS X Download |
GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
It is free software under GPLv2+.
Requested Features:
- Import of Vector NTI...
Platforms: Linux
License: Freeware | Size: 1.7 MB | Download (529): GENtle for Linux Download |
GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
It is free software under GPLv2+.
Requested Features:
- Import of Vector NTI...
Platforms: Windows
License: Freeware | Size: 2.7 MB | Download (512): GENtle for Windows Download |
ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.
Platforms: *nix
License: Freeware | Size: 1.48 MB | Download (51): ASpipe Download |
The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 5.75 MB | Download (47): AVANA - Antigen Variability ANAlyzer Download |
BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 130.91 KB | Download (44): BiasViz Download |
This project aim to build a graphical output of BLAST alignments with more then one sequence database. Using Perl scripts and MySQL.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 54.74 KB | Download (44): BRIAM - Blast Results In A Map Download |
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of...
Platforms: Mac
License: Freeware | Size: 10.24 KB | Download (49): JFinisher Download |
The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 89.51 MB | Download (50): PASA Download |
Prodar is a search application that queries the PDB for candidate structural alignments. The input to the search is a protein backbone structure read from a standard (text) PDB file, and the results returned are based solely on structural similarity of the backbone without any regard to sequence...
Platforms: Windows, Mac
License: Freeware | Size: 618.94 MB | Download (47): Prodar Download |
MayaChemTools is a collection of command line Perl scripts to work with SD files, CSV/TSV text files, Sequence/Alignments files, PDB files, and databases: - splitting, joining, merging, and sorting SD and text files; merging text files into SD files; splitting SD files into MDL MOL files; -...
Platforms: Windows, Mac, *nix, Perl, BSD Solaris
License: Freeware | Download (59): MayaChemTools Download |
This is a Java scrolling applet with several cool features that can enhance your web site. At a specified rate, it reads and reloads from a file and supports auto-wrapped text and images.You can set colors, font face / style / size, left / right / center alignments, Unicode characters, web...
Platforms: Java
License: Freeware | Size: 30.72 KB | Download (40): ScrollUp Download |
AdSense Immediately! is a simple way to generate revenue from your blog using Google AdSense. AdSense Immediately! is a simple plugin to ad adsense ads into the body of your content. It can add one, two or three adsense block to your article body in any google ads format. It alos supports various...
Platforms: PHP
License: Freeware | Size: 10 KB | Download (49): AdSense Immediately! Download |
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: * Is flexible enough to store all the alignment information generated by various alignment programs; * Is simple enough to be easily generated by alignment...
Platforms: Mac
License: Freeware | Size: 368.64 KB | Download (41): SAM Tools Download |
Welcome to the SRMA home page. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed...
Platforms: Mac
License: Freeware | Size: 706.56 KB | Download (46): SRMA Download |
CMView is an intervative contact map visualization and analysis tool. The current version is 0.9.6 Please send feedback to stehr ?*A*t molgen.mpg.de Main features: * Combined contact map and 3D structure view (using PyMol) * Various im- and export options: PDB files, Online PDB, Image...
Platforms: Mac
License: Freeware | Size: 7.1 MB | Download (42): CMView Download |
Recco analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence...
Platforms: Mac
License: Freeware | Size: 1.6 MB | Download (38): Recco Download |