DHGMS Nucleotide

  •        0

T4 (Text Template Transformation Toolkit) Library used by other DHGMS open source projects




Related Projects


Software for storing and analysing bacterial sequence data

SAM tools

SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide efficient utilities on manipulating alignments in the SAM format.


blaSTOR is a Microsoft Access database used to BLAST, store and analyze multiple nucleotide and protein sequences. It has an easy-to-use graphical interface that allows users to perform BLAST operations and organize their data quickly and effectively.


FSA-BLAST is a new version of the popular BLAST (Basic Local Alignment Search Tool) bioinformatics tool, used to search genomic databases containing either protein or nucleotide sequences. FSA-BLAST is twice as fast as NCBI-BLAST with no loss in accuracy.

Biopipe - A set of tools for bioinformatic purposes

Biopipe is a collection of tools for bioinformatics. Features will include: Tools for genomic databank creation and visualization. Web interface for genomic data. Tools for automating bioinformatic pipeline routes. Nucleotide Secondary Structure visualization. Format converters (fasta, embl, dotbracket, etc.)

Santa-sim - SANTA: A simulator of nucleotide and amino acid sequences with selection and recombinati

SANTA simulates the evolution of a population of gene sequences forwards through time. It models the underlying biological processes as discrete components; replication (including recombination), mutation, fitness and selection.

Seqpop - a web interface computing statistics in population genetics

seqpop serves a web interface computing some statistics in population genetics such as the number of segregating sites and Tajima's D. It's hosted on the Google App Engine. Here is an example output. seqpop supports JSON output. Here is an example client in C#. StatisticsThe length of the given alignment The number of segregating sites (Watterson 1975) The average number of pairwi se nucleotide differences (Tajima 1983) Tajima's D (Tajima 1989) Fu and Li's D* (Fu & Li 1993) Fu and Li's F* (Fu &

Poy - Phylogenetic Analysis of DNA and other data using dynamic homology

Welcome to the public source code repository of POYPOY is a phylogenetic analysis program that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned). Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likeli


EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.

Pam-mju - Platform software for nucleotide sequence assembly management

WelcomePAM is a program that can manage raw data, processes and results for various assembly programs and has a GUI (Graphic User Interface) to decrease difficulty of managing many assembly operations. At present, the program supports 4 assembly softwares. Phrap, CAP3, Arachne and TIGR Assembler