Put all your single fasta files in a directory. Open a command interpreter, go to that directory and run the following command: "copy *.fas combinedfile.fas". Your fasta files must have the extension ".fas"; otherwhise modify the "*.fas" part of the command to match your file extensions.

Hi!

If the sequences in the single fasta files represent unique individuals, you could simply copy/paste them into one file in a text editor. If you have too many fasta files (several?), I would suggest switching to a Unix environment; there the task of merging fasta files is straightforward.

Hope this helps,

Best, matthias

I would also suggest switching to a UNIX environment. There are easy ways to install a Virtual Drive on your Windows machine and then run e.g. UBUNTU directly from Windows. I am using the Virtual Box that comes with QIIME (very useful for your other analyses), you can find it together with install instructions here: http://qiime.org/install/virtual_box.html

By creating are shared folder you can easily exchange files between Windows and UBUNTU.

To merge several files use the SHELL, go to your folder where the files are and use the cat command. E.g. to merge seqfile001.fasta, seqfile002.fasta and seqfile003.fasta type "cat seqfile001.fasta seqfile002.fasta seqfile003.fasta > seqcombined.fasta" or if you have more files use "cat *.fasta > seqcombined.fasta"

(a very helpful book to get acquainted with the Linux command line: http://linuxcommand.org/)

For your further analysis you can use QIIME. They have a nice tutorial on their website that explains the steps necessary for an analysis of 454 data: http://qiime.org/tutorials/tutorial.html

Hi Hauke!

I suggest to you to create a txt file, with all the sequence in format FASTA. When you do this, you have listed all the sequences and in the first line in the FASTA file you could add some info about the sequence of the specie.

There are many web pages that pump a fasta file, but the first step is to have them all in one txt archive. In EBI web site if you have the archive make multiple alignments and then makes a likelihood tree.

Another step is to use another program like MEGA 6 or BioEDIT and put all the sequences there and export in the format that you like.

Best wishes.

You can use the script FASconCAT. It will take all .fas files in your folder and create a new alignment with your sequences concatenated based on sequence names. It has a good manual and also I think it is a version for Galaxy that not requires you to use the command line.

https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=3397046a66806440&render_repository_actions_for=galaxy&tool_config=database%2Fcommunity_files%2F000%2Frepo_211%2Fucsb_phylogenetics%2Ffasconcat%2Ffasconcat.xml&changeset_revision=51904e90a6b2

Put all your single fasta files in a directory. Open a command interpreter, go to that directory and run the following command: "copy *.fas combinedfile.fas". Your fasta files must have the extension ".fas"; otherwhise modify the "*.fas" part of the command to match your file extensions.

That is the most awesome and simple solution yet.It even works in windows environments!

Thank you for saving me time & hassle, Leandro!!

@Christian Jessen: how would you do that for files with identical names, and in a loop? E.g. say you have 100 of individuals for which their sequence data was separated into folders where files have the same identical name (corresponding to each Individual)? e.g. Folder A: Indi1.fasta.qz; Indi2.fasta.qz; ... Indi100.fasta.qz; // Folder B: Indi1.fasta.qz; Indi2.fasta.qz; ... Indi100.fasta.q; and I would like to join/cat those files respectively into one single file... THANKS A LOT in advance!

In Unix envs you can put all your fastas in the same folder and type in the command line:

cat /your/path/to/folder/*.fasta > newname.fasta

I think there's an equivalent in windows. like "copy" or "type" but I'm unfamiliar with that.