Man page - alignment-indices(1)

Packages contains this manual

Package:  bali-phy
apt-get install bali-phy

Manuals in package:
• alignment-consensus(1)
• cut-range(1)
• alignment-thin(1)
• alignment-max(1)
• bali-phy-pkg(1)
• bp-analyze(1)
• alignment-draw(1)
• summarize-ancestors(1)
• extract-ancestors(1)
• stats-select(1)
• mctree-mean-lengths(1)
• trees-consensus(1)
• alignment-find(1)
• bali-phy(1)
• statreport(1)
• alignment-indices(1)
• tree-mean-lengths(1)
• pickout(1)
• draw-tree(1)
• alignment-gild(1)
• alignment-distances(1)
• alignment-info(1)
• tree-tool(1)
• alignments-diff(1)
• trees-bootstrap(1)
• mcon-tool(1)
• alignment-cat(1)
• alignment-chop-internal(1)
• alignment-translate(1)
• trees-distances(1)
• bali-subsample(1)
Documentations in package:
• bali-phy

Manual

alignment-indices

NAME
SYNOPSIS
DESCRIPTION
ALLOWED OPTIONS:
REPORTING BUGS:
AUTHORS

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NAME

alignment-indices - Show the alignment in terms of the index of each character in its sequence.

SYNOPSIS

alignment-indices alignment-file [OPTIONS]

DESCRIPTION

Show the alignment in terms of the index of each character in its sequence.

ALLOWED OPTIONS:

-h , –help

produce help message

–align arg

file with sequences and initial alignment

–alphabet arg

set to ‘Codons’ to prefer codon alphabets

-c arg , –columns arg

Ranges of columns to keep, like: 1-10,30-

–invariant arg

print only sites where this site and arg neighbors are invariant.

–differences arg

how many sequences may differ from the majority?

–avoid-gaps arg (=3)

How far from a gap must a column be to be invariant?

–min-constraints arg

Minimum # of constraints per column for a constraint to be emitted

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php .

Please send bug reports to bali-phy-users@googlegroups.com .

AUTHORS

Benjamin Redelings.

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