ACNUC allows to select sequences from many criteria from these three databases, to translate protein-coding genes in protein, and to extract selected sequences in user files. ACNUC is very efficient in providing direct access to coding regions (e.g. protein coding regions, tRNA or rRNA coding regions) of DNA fragments present in GenBank.
Remarque | Run Unix # acnuc ou pour la version X11 xacnuc | Run Web # |
| Version | MAJ | count_base | | |
| cc 30/06/2004 | 2004-06-16 | Download | Doc |
Programme pour compter les ATGC ds une sequence
Remarque | Run Unix # count_base.sh | Run Web # |
| Version | MAJ | count_codon | | |
| none | 2004-08-01 | Download | Doc |
Remarque | Run Unix # count_codon.pl | Run Web # |
DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.
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fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data
The program fastPHASE implements methods described in
Scheet, P and Stephens, M (2006). A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet
fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates. Our experiments suggest that haplotype estimates are slightly less accurate than from PHASE, but missing genotype estimates appear to be similar or even slightly better than PHASE.
Remarque | Run Unix # fastPHASE [options] | Run Web # |
| Version | MAJ | ocount | | |
| 0.4 | 2008-02-07 | Download | Doc |
OCOUNT is a fast C command-line utility that has been written in the course of TETRA's development. It counts oligonucleotides in DNA sequences and computes Markov-Model-based z-scores.
Remarque | Run Unix # ocount | Run Web # |
| Version | MAJ | PROSE | | |
| | Download | Doc |
The relational database PROSE contains protein sequences from Swissprot and Trembl
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RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.
Remarque | Run Unix # start.ratt.sh | Run Web # |
A DNA Sequence Submission and Update Tool
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| Version | MAJ | structure | | |
| 2.3.4 | 2012-12-21 | Download | Doc |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
Remarque | Run Unix # structure | Run Web # |
SeqUence Repository and Feature detectionsNucleotidic sequence production commonly involve several dedicated bioinformatic softwares for sequence basecalling, vector detection, etc.
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WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). It is assumed that traits analysed are continuous and have a multivariate normal distribution.
Remarque http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064953/ ~ http://didgeridoo.une.edu.au/km/download.php?file=hangzhou.pdf| Run Unix # wombat | Run Web # |
