pkg-descr

The LAGAN Toolkit consists of four components:

CHAOS, a pairwise local aligner optimized for non-coding, and other
poorly conserved regions of the genome.

LAGAN, a highly parametrizable pairwise global alignment using local
alignments generated by CHAOS as anchors.

Multi-LAGAN, a progressive pairwise algorithm to produce multiple
sequence alignments.

Shuffle-LAGAN, a novel glocal algorithm that is able to find
rearrangements in a global alignment.

Fast and sensitive multiple alignment of long genomic sequences. BMC
Bioinformatics 2003 4:66.

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple
alignment of genomic DNA. Genome Res 2003 13(4): 721-31.

Glocal alignment: finding rearrangements during alignment. Proceedings
of the ISMB 2003, Bioinformatics 19: 54i-62i.

WWW: http://lagan.stanford.edu/lagan_web/

pkg-plist

lagan/Readmes/README.mlagan
lagan/Readmes/README.FIRST
lagan/Readmes/README.lagan
lagan/Readmes/README.chaos
lagan/Readmes/README.tools
lagan/Readmes/README.shuffle
lagan/Readmes/LICENSE
lagan/anchors
lagan/chaos
lagan/glocal
lagan/mlagan
lagan/order
lagan/anal_gloc.pl
lagan/lagan.pl
lagan/rechaos.pl
lagan/slagan.pl
lagan/utils/Glue
lagan/utils/bin2bl
lagan/utils/bin2mf
lagan/utils/cextract
lagan/utils/contigorder
lagan/utils/cstat
lagan/utils/dotplot
lagan/utils/fa2xfa
lagan/utils/getbounds
lagan/utils/getcontigpos
lagan/utils/getlength
lagan/utils/getoverlap
lagan/utils/rc
lagan/utils/scorealign
lagan/utils/scorecontigs
lagan/utils/seqmerge
lagan/utils/cmerge2.pl
lagan/utils/draft.pl
lagan/utils/mextract.pl
lagan/utils/mf2bin.pl
lagan/utils/mpretty.pl
lagan/utils/mproject.pl
lagan/utils/mrun.pl
lagan/utils/mrunfile.pl
lagan/utils/mrunpairs.pl
lagan/utils/mviz.pl
@dirrm lagan/Readmes
@dirrmtry lagan/utils
@dirrmtry lagan