Results 91–100 of 105 for /biology/.(0.003 seconds)
Integrated environment for Bioinformatics written in Ruby
BioRuby project aims to implement integrated environment for
Bioinformatics by using Ruby.
Tools for manipulating next-generation sequencing data
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
Multiple DNA/protein sequence alignment editor
SeaView is a multiple sequence alignment editor.
You can align DNA/protein sequences from several organisms, and find
out their relative postions in phylogenic tree.
Once SeaView is installed, you can open the on-line help window through
the 'Help' button to learn how to use SeaView.
Example mase files can be found at:
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
Tools for visualising sequence alignments
A suite of tools for visualising sequence alignments.
Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.
Belvu is a multiple sequence alignment viewer and phylogenetic tool.
It has an extensive set of user-configurable modes to color residues
by conservation or by residue type, and some basic alignment editing
capabilities.
Dotter is a graphical dot-matrix program for detailed comparison
of two sequences. Every residue in one sequence is compared to every
residue in the other, with one sequence plotted on the x-axis and
the other on the y-axis.
Single-linkage clustering with Jaccard similarity
Slclust is a utility that performs single-linkage clustering with the option of
applying a Jaccard similarity coefficient to break weakly bound clusters into
distinct clusters.
Very fast matching and alignment of DNA sequences
SSAHA is a software tool for very fast matching and alignment of DNA
sequences. It stands for Sequence Search and Alignment by Hashing
Algorithm. It achieves its fast search speed by converting sequence
information into a `hash table' data structure, which can then be
searched very rapidly for matches.
SSAHA: a fast search method for large DNA databases (2001).
Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9.
PMID: 11591649
Improved tool for transfer RNA detection
tRNAscan-SE was written in the PERL (version 5.0) script language.
Input consists of DNA or RNA sequences in FASTA format. tRNA
predictions are output in standard tabular or ACeDB format.
tRNAscan-SE does no tRNA detection itself, but instead combines the
strengths of three independent tRNA prediction programs by negotiating
the flow of information between them, performing a limited amount of
post-processing, and outputting the results in one of several
formats.
Phylogenetic tree viewer
TreeView X is program to display phylogenetic trees on Unix-like platforms.
It can read and display NEXUS and Newick format tree files (such as those
output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It has a
subset of the functionality of the version of TreeView available for the
Mac Classic and Windows (it is roughly equivalent to version 0.95 of
TreeView).
Flexible read trimming tool for Illumina NGS data
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.
Free, open-source, cross-platform bioinformatics toolkit
Unipro UGENE is multiplatform, open-source software with the main goal of
assisting molecular biologists without much expertise in bioinformatics to
manage, analyze, and visualize their data. UGENE integrates widely used
bioinformatics tools within one common user interface.
UGENE toolkit supports multiple biological data formats and allows the
retrieval of data from remote data sources. It provides visualization
modules for biological objects such as annotated genome sequences, Next
Generation Sequencing (NGS) assembly data, multiple sequence alignments,
phylogenetic trees, and 3D structures.