alignment−cat − Concatenate several alignments (with the same sequence names) end−to−end.
alignment−cat file1 [file2 ...]
Concatenate several alignments (with the same sequence names) end−to−end.
−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
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
BAli−Phy online help: <http://www.bali-phy.org/docs.php>.
Please send bug reports to <bali-phy-users AT googlegroups DOT com>.
Benjamin Redelings.