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MLAGAN(1) User Commands MLAGAN(1)


mlagan - highly parametrizable pairwise global aligner


mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]


Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors.

Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric.


-nested : runs improvement in a nested fashion


The LAGAN_DIR variable specifies the location of the nucmatrix file. It defaults to /usr/lib/lagan, where Debian also place that file.

September 2018 mlagan