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Gblocks file not opened error

I am trying to extract the conserved regions from the MSA file but when I open the file, it is stated file not opened even that was in a FASTA format, and I have tried to convert it to PIR, and didn't work as well. Any suggestions, please?

conserved msa regions
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updated by brian.fristensky brian.fristensky • written by sa.youssef • sa.youssef

As always:

  • a sample (first 5-10 lines) of your MSA file
  • what was the command you used?
  • what was the exact error message?
  • what program did you use for PIR conversion and what was the error message?

Shouldn't some abbreviated guidelines like this be shown at the top of each "New Post" form?

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written by Mensur Dlakic Mensur Dlakic

1 answer

The following will process a FASTA protein file called seqs.fsa at the command line:

Gblocks seqs.fsa -t=p

It will create two files: seqs.fsa-gb (a FASTA file with the selected positions) and seqs.fsa-gb.htm (an HTML report showing the selected positions). The -t parameter would be "d" for DNA.

Gblocks can be run as a point-and-click function in the BIRCH system. An example can be seen in the BIRCH phylogeny tutorial Distance methods.

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written by brian.fristensky brian.fristensky

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