Documentation read from 04/17/2019 22:07:24 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_align_seqs.



    svr_align_seqs [options] < seqs.fa > ali.fa

This script takes a FASTA file from the standard input, aligns the sequences using Clustal, MUSCLE or MAFFT, and writes the alignment in the FASTA format to the standard output.


  Use MUSCLE to align sequences in seqs.fa:

    svr_align_seqs -tool=muscle < seqs.fa > ali.fa

  Use MAFFT to do profile alignment of seqs.fa with seed alignment in profile.fa:
    svr_align_seqs -tool=mafft -profile=profile.fa < seqs.fa > ali.fa

Command-Line Options

Common options


Alignment program to use. Supported tools: mafft, muscle, clustal (default).


FASTA file name of skeleton alignment to be aligned with input sequences. Supported in MUSCLE and MAFFT.


Print tool version information. Supported in MUSCLE and MAFFT.


Use clustal to align ends (zero end gap penalty).

MUSCLE options

  Supported values: anchorspacing center cluster1 cluster2 diagbreak diaglength diagmargin distance1 distance2 gapopen log loga matrix maxhours maxiters maxmb maxtrees minbestcolscore minsmoothscore objscore refinewindow root1 root2 scorefile seqtype smoothscorecell smoothwindow spscore SUEFF usetree weight1 weight2

  Supported flags: anchors brenner cluster dimer diags diags1 diags2 le noanchors quiet sp spn stable sv verbose

MAFFT options

  Algorithm aliases: -alg (linsi | einsi | ginsi | nwnsi | nwns | fftnsi | fftns (D)) (in descending order or accuracy)

  Supported values: aamatrix bl ep groupsize jtt lap lep lepx LOP LEXP maxiterate op partsize retree tm thread weighti

  Supported flags: 6merpair amino anysymbol auto clustalout dpparttree fastapair fastaparttree fft fmodel genafpair globalpair inputorder localpair memsave nofft noscore nuc parttree quiet reorder treeout

Output Format

The standard output is the alignment in the FASTA format.