| Software | |
| Maintenance of this web site ceased by August 31 2018. | |
| PosiGene - is a computer program to scan for positively selected genes (PSGs) on a genome-wide scale based on interspecies sequence comparison and codon based methods.
You can download the software directly from https://github.com/gengit/PosiGene.
Some more supplementary data . (Last update: May 2016) |
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| FRAMA = from RNA-seq data to annotated mRNA assembly.
FRAMA is a transcriptome assembly and mRNA annotation pipeline for eukaryotes.
It utilizies external and newly developed software components to accomplish
common post-assembly tasks. These tasks include gene symbol assignment,
scaffolding of transcripts, fusion detection and CDS as well as mRNA boundary
identification.
FRAMA is free for academic and non-profit use. You can download the software directly from https://github.com/gengit/FRAMA. For commercial usage request commercial license here. (Last update: Oct 2015) |
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| Bucketer Sad = bucketing and searching in second generation sequence data
bucketer is used to extract reads from sequence data with respect to tag-primer pairs
sad is used to search in these data
Bucketer Sad is free for academic and non-profit use. Download source as buck_sad.tgz. (Last update: Dec 2015) |
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| KILAPE = K-masking and Iterative Local Assembly of Paired Ends.
Automated scaffolding and gap filling of /de novo/ genome assemblies.
KILAPE is fast, highly scalable, and can be implemented for large and
complex genomes on modest hardware.
KILAPE is free for academic and non-profit use. You can download the software directly from https://github.com/bdownie/KILAPE. For commercial usage request commercial license here. (Last update: Oct. 2015) |
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| RepARK = Repetitive motif detection by Assembly of Repetitive K-mers.
RepARK.pl is a wrapper script for constructing a repeat library from whole-genome shotgun next-generation reads using Jellyfish and either Velvet or CLC;
published in Nucleic Acids Res 42:e80 (2014).
RepARK is free for academic and non-profit use. You can download the software directly from https://github.com/PhKoch/RepARK. For commercial usage request commercial license here. |
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Roche454ace2caf = Assembly conversation tool roche454ace2caf and
consed2gap are tools to convert assemblies from foreign packages.
Also listed in official Bio-Linux Distribution as "assembly conversion tool".
(Last update: May. 2010)
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kPerl a Sequence Analysis Utility Package.
(Last update: Jul 2008)
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| tuple_plot - a dot plot tool with stochastical background suppression. |
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| GenALA is a toolkit facilitating prokaryotic genome projects by linking GAP4 assembly
and GenColors annotation.
You can download the software directly from ftp://genome.leibniz-fli.de/pub/software/. For commercial usage request commercial license here. (Last update: Febr 2006) |
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MethTools a toolbox to visualize and analyze DNA methylation data.
Downloads available there.
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| Last update: July 18, 2019. |