Man page - alignments-diff(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

alignments-diff

NAME
SYNOPSIS
DESCRIPTION
GENERAL OPTIONS:
INPUT OPTIONS:
OUTPUT OPTIONS:
REPORTING BUGS:
AUTHORS

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NAME

alignments-diff - Align two alignments for comparison.

SYNOPSIS

alignments-diff alignment-file1 alignment-file2 [OPTIONS]

DESCRIPTION

Align two alignments for comparison.

GENERAL OPTIONS:

-h , –help

produce help message

INPUT OPTIONS:

–alphabet arg

set to ‘Codons’ to prefer codon alphabets

OUTPUT OPTIONS:

	–merge		Stack the two alignments into one alignment with duplicate names
	–dual		Write out the two aligned alignments separately

–fill arg (=gap)

blank columns filled with: gap or unknown

-d arg , –differences-file arg

Filename to store differences in AU format

–blocksize arg (=20)

Width of blocks of same color

–classes arg (=1)

Number of groups for non-matching characters

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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