BOL

Hi Mahesh,

There are lots of bioinformatics software, tools and online server for bioinformatics based analysis http://en.wikipedia.org/wiki/Category:Bioinformatics_software , and most of them are useful/applied in plant, animal and microbs based analysis.

However, specifically for Xanthomonas axonopodis datasets, software, tools and other resources, you can visit the following links:

Tools:

http://www.xanthomonas.org/tools.html

http://www.foodmicrobe.com/bioinformatics.pdf

Others:

http://www.xanthomonas.org/genomes.html

http://srnamap.mbc.nctu.edu.tw/

http://csbl.bmb.uga.edu/DOOR/index.php

http://mbgd.genome.ad.jp/

Hope answered your question, and links provided are useful.

Cheers

There are long list of software, but following listed tools will be useful for bacterial based analysis work.

Short read alignment

•bwa – external link:http://bio-bwa.sourceforge.net

•samtools – external link:http://samtools.sourceforge.net

•SHRiMP2 – external link:http://compbio.cs.toronto.edu/shrimp/

•nesoni – external link:http://bioinformatics.net.au/software.nesoni.shtml

•ssaha2 – external link:http://www.sanger.ac.uk/resources/software/ssaha2/

•SMALT – external link:http://www.sanger.ac.uk/resources/software/smalt/

•dindel – external link:http://www.sanger.ac.uk/resources/software/dindel/

•alignment viewers – external link:http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

Assembly

•See Assemblathon 1 post for a systematicly assessed, competitive bake-off of assembly methods

•Velvet – external link:http://www.ebi.ac.uk/~zerbino/velvet/

•SOAPdenovo – external link:http://soap.genomics.org.cn

•ABySS – http://www.bcgsc.ca/platform/bioinfo/software/abyss

•Vmatch – external link:http://jermdemo.blogspot.com/2009/11/using-vmatch-to-combine-assemblies.html

Annotation & browsing

•Artemis, ACT, BamView, DNA Plotter – external link:http://www.sanger.ac.uk/resources/software/artemis/

Genome alignment

•MUMmer

•Mauve

Phylogenetics & population genetics

•BEAST – Bayesian inference, divergence date estimation

•RAxML – fast maximum likelihood inference, great for large datasets

•phylip – Parsimony, likelihood, minimum evolution, etc etc… the grandaddy of phylo software, best for small data sets

•PAML – maximum likelihood phylogenetic & evolutionary inference

•PhyML – maximum likelihood, run online here

•SplitsTree4 – brilliant Java-based app from Daniel Huson, builds phylogenetic networks and trees of nearly every kind

•Dendroscope – Java-based tree viewer app from Daniel Huson, lots of alternative views available and can build consensus tree or network from sets of trees

•FigTree – tree viewer app, radial or dendrogram, can load annotations, great for viewing BEAST trees

•iTOL (interactive tree of life) – online tool, load up your tree file and associated data for an amazing array of visualisation options. great for overlaying data (eg gene content, protein domain structures, etc) on a tree

•Hal – phylogenetic analysis of whole genomes

•PhyloGeoViz – visualize haplotype frequencies (as pie charts) over an interactive map (google maps/google earth)

16S & Metagenomics

•QIIME – external link:http://qiime.sourceforge.net/

•NIH Human Microbiome Project (data, protocols, software) – external link:http://www.hmpdacc.org/