[Bioperl-l] Is there a "combine" method that would combine several sequence alignments to a single alignment?
gregonomic at yahoo.co.nz
Mon Nov 21 07:00:50 EST 2011
I've attached a simple script (concatenate_alignments.pl) I wrote to concatenate alignments.
It can be a bit of a memory hog if you have long alignments or large numbers of sequences; otherwise you should be OK.
concatenate_alignments.pl -o <output_alignment> <input_alignment_1> <input_alignment_2> <... input_alignment_n>
If you want to insert a string between the concatenated sequences, you can use the -j option (eg. -j '---').
From: Dave Messina <David.Messina at sbc.su.se>
To: Tao Zhu <tzhu at mail.bnu.edu.cn>
Cc: BioPerl <bioperl-l at lists.open-bio.org>
Sent: Monday, 21 November 2011 7:58 PM
Subject: Re: [Bioperl-l] Is there a "combine" method that would combine several sequence alignments to a single alignment?
No, I don't believe such a method exists. Could you describe what you are
wanting to do? Perhaps there is another way to do it.
On Mon, Nov 21, 2011 at 06:17, Tao Zhu <tzhu at mail.bnu.edu.cn> wrote:
> I can use the "slice" method to split a single sequence alignment into
> several subalignments. Then is there a corresponding "combine" method to
> combine such subalignments back?
> Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
> 100875, China
> Email: tzhu at mail.bnu.edu.cn
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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