Software

 

  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)

  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)

  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)

  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)

  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.

  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)

  kPerl a Sequence Analysis Utility Package.
(Last update: Jul 2008)

  tuple_plot - a dot plot tool with stochastical background suppression.
Current version v1.1.1 (2008-12-08). Download source as *.zip or *.tgz.

  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)

  MethTools a toolbox to visualize and analyze DNA methylation data.
Downloads available there.

    Last update: February 22, 2017.