alignment−cat

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 AT googlegroups DOT com>.

AUTHORS

Benjamin Redelings.