I want to perform multiple alignments of genes to a reference sequence using Muscle (https://www.drive5.com/muscle/) locally. The reference sequence is stored in a fasta file, and every chromosome is stored as different fasta sequence within this fasta file. To give you examples:
**gene.fa** >gene1 ATGATG.... **reference_genome.fa** >chr1 ATCGTGA... >chr2 GTACTAA... >chr3 ATCTGTC...
When I go through Muscle manual, it mentions the command for performing alignments to be something like:
muscle -in seqs.fa -out seqs.afa
All the input sequences are to be stored within
seqs.fa (if I understand it correctly). My question: in my case how do I create the
seqs.fa file, given that the chromosomes themselves are stored as different fasta sequences?
Any help would be appreciated!