I have a concatenated MS alignment of more then 3000 genes in fasta format.
I would like to split this alignment in 10-20 files, equally divided if it possible.
In my MSA I have 30 seqs, and each seq is made of milions of bp.
>1 ATTGCTGAAACGGCTTTGAAAAGGGCGGAAAATCTTTCTGGTGGT [..] >2 ATTGCTGAAAC----GGCTTTGAAAAGGGC----GGAAAATCTTTCTGGTGG [..] >3 ATTGCTGAAAC----GGCTTTGAAAAGGGC----GGAAAATCTTTCTGGTGGT [..] >4 GATGAGCCGATTGCTTCGCTGGATCCGATGAATGCGCAGGTGGTGATGGACGCTCTTAAG [..] ........
Now I would like to split this file in multiple files having chunks of the MSA. for example file1 from position 1 to 300; file 2 from position 301 to 600; file 3 from 6001 to 900; and so on.
I could not find a way of doing that, any suggestion?
The problem is that most of the tools only split multiple fasta in different files or split single sequences.
PS: I do not have available the original single MSA