I have 2504 cds sequences in a fasta format which I want to combine into a single fasta file and run the alignment on them !
Help Required !!!!!!
A: Multiple sequence alignment
Assuming your files have an common suffix (i.e 1.fasta, 2.fasta, 3.fasta...)
cat *.fasta > total.fasta
Then you can run the program of your interest (ClustalW, etc..)