Geneious is a good one. You can download reference sequences from GenBank and compare them in this program.

I find that MEGA is a very good free software. It allows you a fine set up of the alignment parameters, it may perform additional analyses on the multi-alignments (distances, etc.), and it let you export data in a number of alignment formats (such as nexus and phyllip) which you could use to infer phylogenetic trees.

Furthermore it is quite stable, as it crashes very seldom.

I use MAUVE and ACT both are free and have pros and cons, but if I have to choose, I´ll settle for MAUVE. It works great with bacterial genomes, I don´t know how it will perform with bigger genomes.

by the way, MEGA is for smaller sequences, not genomes.

the muscle algorithm is most appropriate i find, regardless of which program you run it in- I will definitely recommend MAUVE though - good visualisation and downstream analysis options.

I agree with Geneious. Mauve you should only use if you expect rearrangements on bigger sequence fragments 20k+. Another nice tool is MegALign (DNASTAR). In combination with MEGA or DNAsp one can get nice phylogenetic distribution results/output but many of them are available with various Geneious Plugins.

Greets

Martin

Thanks all for the input. Agreed that MEGA is a great program but most effective for shourter sequences. I'll have to explore Mauve - DNASTAR acknowledges its utility by including link for it in their Navigator software. Another option I'm exploring is the MUMmer software package (mummer.sourceforge.net) and specifically the NUCmer utility. It looks like you can use this program to align many sorts of sequence (flat files, fastas, contigs or no) to almost any other sort of sequence. The interface and visualization is rudimentary compared to some of the more modern, or more expensive, options suggested, but it looks like it does exactly what we need it to do. Neafsey et al (Nat Genetics, 2012) use MUMmer to do something similar.

Berte - good point. I was just beginning to realize that MUMmer will only align two genomes, in whatever form. Good idea about Mugsy - I'll try it out.

I recommend a recent review "Whole-genome alignment" by Colin Dewey (in the book I edited "Evolutionary Genomics: Statistical and Computational Methods"):

http://www.springerlink.com/content/g274434068345822/#section=1046243&page=1

I recommend the Mugsy, an useful tool for genome scale multiple alignment

I recommend LASTZ and Multiz. Which tool did you ended up using?

how to use mugsy for 16 genomes of 30 Mb each

Please i want to do comparative analysis of 100 plasmids. How do i go about it. Which tool can I use?

MAUVE is a great tool and easy to learn; ANVIO is also a great software, although I has a somewhat steep learning curve, but well worth the effort to implement it as it is much more complete.

I would recommend 2 tools: install PathwayTools on your computer and start playing with it or install MAUVE. MAUVE will stall above 20 genomes and Pathway Tools will stop at 70. If you have more genes, you should try NCBI BLAST->COBALT as it can easily handle 100 genes.

I personally use Biocyc (Phoenix Bioinformatics) due to its integration with the rest of tools. It is a paid service but relatively cheap for academia and industry.

UNCCH has funds to set it up and you should ask Dept. head to install it. Your PI can also install it as a personal subscription or as a lab tool from grant's money.

In my opinion, it is not worth reinventing the wheel by looking at every single lab and testing their solutions. They simply are below par for the overall picture.

Best regards,

Wes