Diploid Genome Sequence
The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
Platforms: Mac, Solaris, Linux
License: Freeware | Size: 339.36 MB | Download (42): RDXplorer Download |
The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
Platforms: *nix
License: Freeware | Size: 339.27 MB | Download (34): RDXplorer Download |
The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence...
Platforms: Windows
License: Freeware | Size: 8.4 MB | Download (418): Integrated Genome Browser Download |
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data. Genome Workbench can display sequence data in many ways,...
Platforms: Mac
License: Freeware | Size: 35.54 MB | Download (40): Genome Workbench Download |
UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. for WindowsAll
Platforms: Windows
License: Freeware | Download (467): UGENE Download |
Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based web interface is also available. Please cite: Lee, W., Chen S.L. BioTechniques 33:1334-1341 (Dec 20
Platforms: Windows, Mac, Linux
License: Freeware | Size: 43.83 KB | Download (44): genome-tools Download |
UML::Sequence is a Perl module to render UML sequence diagrams, often by running the code. SYNOPSIS use UML::Sequence; my $tree = UML::Sequence->new(@methods, @outline, &parse_method); print $tree->build_xml_sequence(Title); To use this package, or see how to use it, see genericseq.pl...
Platforms: *nix
License: Freeware | Size: 122.88 KB | Download (159): UML::Sequence Download |
UML::Sequence::JavaSeq is a Perl module for use with genericseq.pl script, works on compiled Java programs. SYNOPSIS genericseq.pl UML::Sequence::JavaSeq Hello.methods Hello > Hello.xml seq2svg.pl Hello.xml > Hello.svg OR genericseq.pl UML::Sequence::JavaSeq Hello.methods Hello |...
Platforms: *nix
License: Freeware | Size: 122.88 KB | Download (92): UML::Sequence::JavaSeq Download |
Chart::Sequence is a sequence Perl class. SYNOPSIS use Chart::Sequence; my $s = Chart::Sequence->new( Nodes => [qw( A B C )], Messages => [ [ A => B => "Message 1" ], [ B => A => "Ack 1" ], [ B => C => "Message 2" ], ], ); # or # my $s = Chart::Sequence->new( SeqMLInput =>...
Platforms: *nix
License: Freeware | Size: 15.36 KB | Download (105): Chart::Sequence Download |
Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in...
Platforms: *nix
License: Freeware | Size: 2.3 MB | Download (122): Sequence Analysis Download |
The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.
Platforms: Linux
License: Freeware | Size: 5.7 MB | Download (473): Celera Genome Browser for Linux Download |
The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.
Platforms: Linux
License: Freeware | Size: 5.7 MB | Download (446): Celera Genome Browser Download |
Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
Artemis is written in Java, and is available for UNIX, Macintosh and...
Platforms: Windows, Mac, Linux, Java
License: Freeware | Size: 10 MB | Download (452): Artemis Download |
Short Sequence Location Mapper loads the sequences, then aligns them and finally graphs and tables can be generated for one or more datasets at the same time.
SSLM typically works with a BLAST data output file of short Solexa reads mapped to RNA subjects (for example pre-miRNA sequences).
The...
Platforms: Windows
License: Freeware | Download (471): Short Sequence Location Mapper Download |
Creates an Excel spreadsheet report about the video clips, audio clips and markers you've used in your edited sequence. The report includes sheets for: Clips, Sequence Markers, Clip Markers, Clip Filters, and Reels.
Sequence Clip Reporter takes the tedious work out of creating clip usage reports...
Platforms: Mac
License: Freeware | Size: 3.6 MB | Download (479): Sequence Clip Reporter for Mac OS Download |
3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 4.09 MB | Download (45): 3D Genome Tuner Download |
The fastest way to remove duplicates from a sequence depends on some pretty subtle properties of the sequence elements, such as whether they're hashable, and whether they support full comparisons. This script defines the unique() function that tries three methods, from fastest to slowest,...
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (52): Remove duplicates from a sequence Download |
This script contains a function that given a sequence and a number n as parameters, returns the th permutation of the sequence (always as a list).
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (54): Getting th permutation of a sequence Download |
This script allows you to split up a sequence in same-size (if possible) parts.
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (51): Splitting up a sequence Download |
Getting min/max in a sequence script allows you to find the min/max value in a sequence as compared to a reference.
Platforms: Windows, Mac, *nix, Python, BSD Solaris
License: Freeware | Download (51): Getting min/max in a sequence Download |