The MUSCLE command line doesn't have an option for returning the pairwise sequence alignment. Is there a way to get those alignment(in python)?
for example if I have three sequences Seq1,Seq2 and Seq3:
Tt gives me the aligned sequences as follows:
s1 and s2
s1 and s3
s2 and s3
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bioinformaticsm28 •
IMO you'll have to split your sequences into separate input files and run one of these tools for each pair. MUSCLE does not have the option to do combinatorial pairwise alignment.
Thank you.If I sperate may sequencs , may be I lost the value of multiple alignment
OK. Thank you.I try to use Emboss, when I use NEEDLE, I get the following errors:
From the window of saved Results
Error: Failed to open filename '-noendweight'
Error: Unable to read sequence '-noendweight'
Died: needle terminated: Bad value for '-bsequence' with -auto defined
and this error from the file stderrfile :
Died: Value required for '-bsequence' before '-gapopen'
I do it with the software mEMBOSS
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bioinformaticsm28 •
It is mEMBOSS a GUI application
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bioinformaticsm28 •
This is what I get
Error: Failed to open filename '-noendweight'
Error: Unable to read sequence '-noendweight'
Died: needle terminated: Bad value for '-bsequence' with -auto defined
No, it didn't
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bioinformaticsm28 •
I think there is a EMBOSS command named "dismat". You could also use python to call the command needle to get pairwise alignments. However, it would be very slow. I suggest to use vsearch:
vsearch --allpairs_global fastafile --acceptall
vsearch offers a variety of output formats. Disclaimer: I am a member of the vsearch team.
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Frédéric Mahé
Thank you. It works on GNU/Linux or OS X, but not on windows.
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bioinformaticsm28 •
OK.thank you
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bioinformaticsm28 •
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