Wikiomics:Genome aligners

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

=Aligners=

MUMmer
web: http://mummer.sourceforge.net/

version: MUMmer3.22.tar.gz from 2009-09-21

LAGAN Toolkit
http://lagan.stanford.edu/lagan_web/index.shtml ver 2.0 from 2006
 * LAGAN
 * M-LAGAN
 * Shuffle-LAGAN

Vmatch
http://www.vmatch.de/

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

documentation: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html

New releases: http://www.bx.psu.edu/~rsharris/lastz/newer/

last
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. lastdb -c -s20G -v genome1_db genome1_sequence.fa
 * 1) create database from one of the genomes (larger?) on a machine with > 20GB free RAM to speed up the process

lastal -o genome2_vs_genome1.maf -v genome1_db genome2_sequence.fa
 * 1) align the genomes with maf output

YASS
web: http://bioinfo.lifl.fr/yass/

last release: pre-release v1.14 build Apr 15, 2010

paper; doi:10.1093/nar/gki478

spliced seeds, see also links to hedera & iedera programs on YASS page.

Cgaln
web: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/cgaln/

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).

FEAST
web: http://monod.uwaterloo.ca/feast/

last release: feast-105-bin.tar.gz

more sensitive but slower than lastz, new tool not widely tested.

MAUVE
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.

Spines
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"

Mercator
Multiple Whole-Genome Orthology Map Construction

http://www.biostat.wisc.edu/~cdewey/mercator/

latest release: cndsrc-2010.10.11.tar.gz

Enredo-Pecan-Ortheus pipeline
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/

FSA
http://orangutan.math.berkeley.edu/fsa/

latest version: fsa-1.15.5.tar.gz (10.1 MB)

paper: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000392

Mugsy
http://mugsy.sourceforge.net/

(bacterial genomes)

AuberGene
http://www.ibi.vu.nl/programs/aubergenewww/ Probably most suitable for aligning a particular gene locus.

=Alignment visualisation=
 * VISTA
 * MULAN
 * GeLo
 * Gmaj

Novel:
 * Strudel http://bioinf.scri.ac.uk/strudel/

=Supporting tools=

http://dagchainer.sourceforge.net/
 * DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes (Perl)

=Useful links=
 * how to create a synteny map between two genomes: http://synteny.cnr.berkeley.edu/wiki/index.php/SynMap

=Conservation scores=

phastCons
http://compgen.bscb.cornell.edu/phast/

GERP
http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html

Scone
http://ika.bwh.harvard.edu/scone/

=Varia=

SiPhy
web: http://www.broadinstitute.org/genome_bio/siphy/

article: http://bioinformatics.oxfordjournals.org/content/25/12/i54.short