Man page - alignment-translate(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-translate

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

---

NAME

alignment-translate - Translate a DNA/RNA alignment into amino acids.

SYNOPSIS

alignment-translate [OPTIONS] < sequence-file [OPTIONS]

DESCRIPTION

Translate a DNA/RNA alignment into amino acids.

ALLOWED OPTIONS:

-h , –help

Produce help message

-g arg (=standard), –genetic-code arg (=standard)

Specify alternate genetic code.

-f arg (=1), –frame arg (=1)

Frame 1, 2, 3, -1, -2, or -3

-r , –reverse

Just return the reverse

-c , –complement

Just return the complement

-t arg (=yes), –translate arg (=yes)

Translate the sequences

EXAMPLES:

Translate DNA or RNA to amino acids in reading frame 1:

% alignment-translate < dna.fasta > aa.fasta

Give the reverse complement without translation:

% alignment-translate -rc --translate=no < dna.fasta > dna2.fasta

The following commands are identical:

% alignment-translate --frame=-2 < dna.fasta > aa2.fasta
% alignment-translate -rc --frame=2 < dna.fasta > aa2.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.

---