Man page - alignment-cat(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-cat

NAME
SYNOPSIS
DESCRIPTION
ALL OPTIONS:
EXAMPLES:
REPORTING BUGS:
AUTHORS

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NAME

alignment-cat - Concatenate several alignments (with the same sequence names) end-to-end.

SYNOPSIS

alignment-cat file1 [ file2 ...]

DESCRIPTION

Concatenate several alignments (with the same sequence names) end-to-end.

ALL OPTIONS:

-h , –help

Produce help message

–output arg (=fasta)

Which output format: fasta or phylip?

-c arg , –columns arg

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

-t arg , –taxa arg

Taxa to keep, comma-separated

-p , –pad

Add gaps to make sequence lengths identical

-r , –reverse

Reverse the sequences

-e , –erase-empty-columns

Remove columns with no characters (all gaps).

–missing arg (=-?)

What letters are not characters (e.g. gaps)?

–strip-gaps

Remove all non-character letters from sequences.

–reorder-by-tree arg

Reorder the sequences given a tree

–use-root

use the root specified in the tree file to reorder

–reorder-by-alignment arg

Reorder the sequences following an alignment

–align-by-amino arg

Arrange nucleotides into codon alignment

EXAMPLES:

To select columns from an alignment:

% alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
% alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
% alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta

To concatenate two or more alignments:

% alignment-cat filename1.fasta filename2.fasta > all.fasta

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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