Thank you for asking this question. Right now I have the same query...
http://lagan.stanford.edu/lagan_web/index.shtml
Supports very large geonme wide sequences
some info on (Brudno et al. Genome Research, 2003)
http://mummer.sourceforge.net/
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
Can u please explains me how to install and use mummer in simple way..
You should check the original paper where the human genome were aligned with mouse genome (http://genome.cshlp.org/content/13/1/103.long). Also, to be up to date, I would suggest you to use Lastz, which is the improved version of blastz. To use it, everything is explained here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
It's very easy to use, it takes as input fasta files.
MAFFT and MAUVE are also good options for multiple large sequence alignments - both are relatively fast, easy to use and display easy to read output.
while iam running mauve, the programme was stopped by showing massage "Excited with error 255".....can u pls expalain me how can i sort out the error...
Your problem discussed here.
Might find solution.
http://sourceforge.net/mailarchive/forum.php?set=custom&viewmonth=&viewday=&forum_name=mauve-users&style=nested&max_rows=50&submit=Change+View
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