Here is the list of available command line software.
Categories
All
Expression analysis
- Librairies and other tools
- SNP and structural variations
- Repeats
- Proteins
- Phylogeny / Metagenomic
- Sequences cleaning
- Pattern
- Genetic map
- Assembly
- ncRNA
- Annotation
- Sequences alignment
- Genomic association studies
- Mathematic
- Population genetics
- ChIP-Seq analysis
- RAD-Seq analysis
Nucleic acid folding
02.05.2013
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://www.bioinformatics.babraham.ac.uk/projects/bismark/
Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://www.bioinformatics.babraham.ac.uk/projects/bismark/
Category: Genetic map
02.09.2010
CarthaGène is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGène can handle data made up of several distinct populations which may each be either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds and/or radiated hybrids (haploid and diploid data).
http://www.inra.fr/mia/T/CarthaGene/
carthagen
CarthaGène is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGène can handle data made up of several distinct populations which may each be either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds and/or radiated hybrids (haploid and diploid data).
http://www.inra.fr/mia/T/CarthaGene/
Category: Genetic map