Taxonomic

Taxonomic Search Engine is a test bed for a web service approach to federating taxonomic name databases. Written in PHP, which is a free PHP search engine software. It takes your query and talks to a number of different databases, asking each one whether they contain that name.

A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.

PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.


Platforms: Windows, Mac, Linux

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. More information can be found at http://rdp.cme.msu.edu/.


Platforms: Windows, Mac, Solaris, Linux

This demo illustrates a simple approach to perform taxonomy annotation of BLAST hits. It requires three taxonomy files gi_taxid_prot.dmp, names.dmp and nodes.dmp, which can be downloaded from the NCBI taxonomy FTP site.


Platforms: Matlab

[EN] This module extends the Nice Menus module (http://drupal.org/project/nice_menus).With him, Nice Menus module can display taxonomic dictionaries, as usual menu. This module is not an independent d-deOCt for his work requires Nice Menus.


Platforms: PHP

Taxonnerator is a software package for carrying out simple similarity-based annotation of clustered barcode sequence data produced by jMOTU. It generates taxonomic annotation for MOTU by BLASTing representative sequences against a preformatted database of sequences from known organisms (available...


Platforms: Mac

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU). If you are not sure what a MOTU is, please see the DNA Barcoding pages on our website. jMOTU does the following: *reads input sequences in FASTA or NEXUS format *calculates...


Platforms: Mac

ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm.


Platforms: *nix

Taxtastic is software written in python used to build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information. . quickstart . full documentation


Platforms: *nix

Sembrowser is a prototype of a semantic faceted file manager for KDE 4. The faceted side panel is based on the Nepomuk technology and libraries. A faceted classification system allows the assignment of multiple classifications to an object, enabling the classifications to be ordered in multiple...


Platforms: *nix

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data....


Platforms: *nix

Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...


Platforms: *nix

A powerful and user-friendly graphical software designed to conduct large scale exploration of biological sequence databanks and related information (functional, taxonomy, pathways, mutations, etc). KoriBlast can be used for a wide range of applications in genomics and proteomics, such as: full...


Platforms: Mac

This function contains the well known greedy algorithm for solving Set Cover problem (ChvdodAtal, 1979), with two small modifications:* In case of more than one possible choice at a certain step, the biggest set is chosen;* Once the solution is found, we check the selected sets to find a better...


Platforms: Matlab