Hello everyone,
I am thinking of working with information of different genes, and concatenate their sequences... So I was thinking are there any software to easily make your sequence matrix with different genes for the same samples? Right now I am using Geneious and concatenating the sequences one by one, but as I will start to work with a lot of samples I don't know if there are any simpler way.
Thank you in advance,
Hamid.
Hello Hamid,
I understand that your aim is to obtain a single multi-fasta file from many fasta files that contain one sequence each one, is that right.
If so, in Mac or Linux you can use the cat command from the terminal. For instance:
cat *.fasta > all_sequences.fasta
In windows replace cat for type.
Best,
Juan
Thank you Juan Luis, actually in Geneious I can do the same and concatenate sequences with the same names one by one, but I was wandering if there is something easier for really large matrix, to not have to change names in the alignments and for example generate the matrix directly with GB accession numbers....
Thank you anyway man,
Hamid.
Dear Andrii,
I took a look to CLC, but I don't see how it can help more than Geneious! But thank you anyway.
Hamid.
I use a simple python script that i build for concatenating using the bio.nexus plugin. To make it work you have to have the name in each of your alignment files exactly the same for the corresponding sequences. Than you can concatenate all the sequences within seconds.
Just let me know your mail address and I can send you the file and some instructions.
Theo
Hi Theodor,
I guess I can do the same on Geneious... But anyway yes please send me the file and instructions, [email protected], it is much better to not depend only on one software :)
Thank you,
Hamid.
- Badges
- Science method
- Similar topics
- Biological Science
- Genetics
- Genetic Analysis
- genetic techniques
- Sequencing