Command line to add algorithm option for MAFFT using GUIDANCE2

Question

[NicoN64]

Hello,

I am using guidance 2 with MAFFT to create alignments of thousand of genes. I am working on a cluster and submit job as a array with a bash command. I would like to test different algorithms available with MAFFT for the alignment (--localpair / --genafpair / --globalpair). On Guidance website they indicate that there is an option for the parameter: --MSA_Program They give an example with PRANK: --MSA_Param -F (I suppose). However in a perl script I they say that you have to add two \ before '-'

So is it correct for MAFFT to add the command: --MSA_Param \--localpair ?

I did found information in the log file created, that MAFFT was using --localpair. What algorithm by default Guidance use for MAFFT?

Thanks

[milesdroberts]

This question is somewhat old, but I've run into the exact same problem! Here are all of my attempts to correctly specify the --MSA_Param argument in order to set the "maxiterate" parameter to 1000 and enable the "localpair" option when using GUIDANCE2 (V2.02) on a command line:

--MSA_Param \-\-maxiterate 1000 \-\-localpair

--MSA_Param \--maxiterate 1000 \--localpair

--MSA_Param --maxiterate 1000 --localpair

--MSA_Param \-maxiterate 1000 \-localpair

\-maxiterate 1000 \-localpair

\-\-maxiterate 1000 \-\-localpair

--maxiterate 1000 --localpair

So far, none of them have worked. I've emailed the creators of GUIDANCE2 for assistance and I'll let you know if they respond.

EDIT: I think I figured it out! Specifying my desired GUIDANCE2 options in this way exactly didn't return an error

--MSA_Param \\--localpair \\--maxiterate 1000

In my case, I had to specify the maxiterate parameter after the localpair parameter. Otherwise, GUIDANCE would interpret the characters "localpair" as input to the maxiterate parameter. An return with a "non-integer argument" error.

EDIT #2: The creator of GUIDANCE2 got back to me and said the following:

Please wrap the --MSA_Param arguments also with a ' or " around all arguments (separated by whitespace) to designate they all should be passed to the MSA algorithm as a single argument. For example, in your command this would apply as follows:

--MSA_Param '\-\-maxiterate 1000 \-\-localpair'

This answer is a couple years too late, but I hope it's helpful to someone :)

[NicoN64]

Nice! Thanks for posting the solution.

[Sej Modha]

According to the documentation provided online, MAFFT uses L-INS-i - Iterative refinement methods using WSP and consistency scores when --localpair option is used.

PS: Also check out the parallelized version of MAFFT if you are trying to align a large number of sequences.

[NicoN64]

Thanks, but my question is how to write correctly the bash script for Guidance2 to be able to indicate the algorithm for MAFFT:

perl /share/apps/centos7/guidance/2.02/www/Guidance/guidance.pl --seqFile ~/Guidance/MSA/$INPUTFILE --msaProgram MAFFT --MSA_Param \--localpair --seqType codon --dataset $FILENAME --outDir ~/Guidance/MAFFT_Codon/$OUTPUTS

or

perl /share/apps/centos7/guidance/2.02/www/Guidance/guidance.pl --seqFile ~/Guidance/MSA/$INPUTFILE --msaProgram MAFFT --MSA_Param \\--localpair --seqType codon --dataset $FILENAME --outDir ~/Guidance/MAFFT_Codon/$OUTPUTS

Tested the two by seems to not working. Guidance log file only indicate Align: mafft --reorder --amino --quiet

I don't know which algorithm is used.

[Sej Modha]

I am not sure this would work but have you tried \-\-localpair?