mlagan1
Highly parametrizable pairwise global aligner
Usage
mlagan seqfile_1
seqfile_2
[seqfile_63]
[-parameters]
Overview
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.
Options
-nested: runs improvement in a nested fashion
-postir: incorporates the final improvement phase
-lazy: uses lazy mode
-translate: use translated anchors
-fastreject: use fast rejection (tuned for human/mouse or closer)
-verbose: give debug output
-tree"(...)" : runs with given phylogenetic tree
-out"filename": outputs to filename
-nucmatrixfile"filename": uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt
-version: prints version info
-nested : runs improvement in a nested fashion
-postir: incorporates the final improvement phase
-lazy: uses lazy mode
-translate: use translated anchors
-fastreject: use fast rejection (tuned for human/mouse or closer)
-verbose: give debug output
-tree"(...)" : runs with given phylogenetic tree
-out"filename": outputs to filename
-nucmatrixfile"filename": uses given substitution matrix instead of $LAGAN_DIR/nucmatrix.txt
-version: prints version info
Environment
The LAGAN_DIR variable specifies the location of the nucmatrix file. It defaults to /usr/lib/lagan, where Debian also place that file.