List of programs used for large scale DNA alignment. At the moment the statements are mostly from web sites of programs in question.
For introduction read: Lyons and Freeling "How to usefully compare homologous plant genes and chromosomes as DNA sequences" 2008 Also: Parameters for accurate genome alignment by Frith et al BMC Bioinformatics 2010, 11:80 http://www.biomedcentral.com/1471-2105/11/80
version: MUMmer3.22.tar.gz from 2009-09-21
http://lagan.stanford.edu/lagan_web/index.shtml ver 2.0 from 2006
Free of charge non-commercial license (requires faxing).
lastz (successor of blastz)
web site: http://www.bx.psu.edu/~rsharris/lastz/
latest stable release: 2010-Jan-12
New releases: http://www.bx.psu.edu/~rsharris/lastz/newer/
http://last.cbrc.jp/ last release: last-159.zip 14-Feb-2011 18:59 340K
Compare two vertebrate genomes (Human vs. mouse: 1 day on 1 CPU) copes more efficiently with repeat-rich sequences can align a large number of sequences (i.e. next gen sequencing data to genome)
Use softmasked input sequences.
#create database from one of the genomes (larger?) on a machine with > 20GB free RAM to speed up the process lastdb -c -s20G -v genome1_db genome1_sequence.fa #align the genomes with maf output lastal -o genome2_vs_genome1.maf -v genome1_db genome2_sequence.fa
last release: pre-release v1.14 build Apr 15, 2010
spliced seeds, see also links to hedera & iedera programs on YASS page.
last release: Cgaln-1.0.0.tar.gz
Two step aligner (first at the blocks then nucleotide levels). According to authors, fast and memory efficient. Suitable for bacterial genomes and mammalian chromosomes on a desktop computer( untested dk).
last release: feast-105-bin.tar.gz
more sensitive but slower than lastz, new tool not widely tested.
multiple genome alignment http://asap.ahabs.wisc.edu/mauve/ last release: 2.3.1, from November 11th 2009. Java application with GUI. Simple to use, producing colorful graphic. Output gets too cluttered with too many / too divergent sequences.
software collection from Broad http://www.broadinstitute.org/science/programs/genome-biology/spines latest release: spines-1.11.tar.gz from 2010-10-28
- Satsuma "highly parallelized program for high-sensitivity, genome-wide synteny"
- Papaya "an all-purpose alignment tool for less diverged sequences"
- SLAP "context-sensitive local aligner for diverged sequences with large gaps"
Multiple Whole-Genome Orthology Map Construction
latest release: cndsrc-2010.10.11.tar.gz
Several programs used for aligning eukariotic genomes at ENSEMBL.
- Enredo: http://www.ebi.ac.uk/~jherrero/downloads/enredo/
- Pecan: http://www.ebi.ac.uk/~bjp/pecan/
- Ortheus: http://www.ebi.ac.uk/~bjp/ortheus/
latest version: fsa-1.15.5.tar.gz (10.1 MB)
http://www.ibi.vu.nl/programs/aubergenewww/ Probably most suitable for aligning a particular gene locus.
- DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes (Perl)
- how to create a synteny map between two genomes: http://synteny.cnr.berkeley.edu/wiki/index.php/SynMap