MUSCLE alignment - aligning whole genome with gene sequences

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Hello all,

I want to perform multiple alignments of genes to a reference sequence using Muscle (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!


alignment


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