[EMBOSS] shuffleseq for multifasta?

[Anandkumar Surendrarao]

Greetings!

I am new to EMBOSS, and trying to use shufflseq to randomly shuffle entire
genomes (one-by-one). My input genomic sequences are in multifasta format.
And I wish to retain the same multifasta format for the output file as
well, containing the shuffled DNA sequences.

>From the information at
http://emboss.sourceforge.net/apps/cvs/emboss/apps/shuffleseq.html, it
appears to me that FASTA format for neither input not output is supported.
Am I mistaken?
OR
Is there a way to specify (multi)FASTA as both input and output formats?

In one run that I completed with a genome assembly with 5 chromosmes - Chr1
... Chr5, the syntax I used was:
shuffleseq -sequence Athaliana_167_TAIR9.fa.shIDscleaned-up -outseq
Athaliana_167_TAIR9_EmbossShuffled.fas

Strangely, in the output file, the fasta headers were all repetitive Chr1.
Hence my confusion. Could someone please clarify what my input formatting
should be and the correct syntax?

Thanks, in advance, for your help.

Sincerely,
Anand
_____
*Anandk*umar *S*urendra*rao*, PhD
+1.530.574.5134
+91.91760.70887
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