#!UGENE_WORKFLOW #Read sequences, join them into alignment, perform alignment algorithm and save result workflow "Join and align sequences"{ read-sequence { type:read-sequence; name:"Read sequences"; merge-gap:10; mode:0; } sequences-to-msa { type:sequences-to-msa; name:"Join sequences into alignment"; } muscle { type:muscle; name:"Align with MUSCLE"; max-iterations:-1; mode:0; range:"Whole alignment"; stable:true; } write-msa { type:write-msa; name:"Write alignment"; document-format:clustal; write-mode:2; } .actor-bindings { sequences-to-msa.out-msa->muscle.in-msa muscle.out-msa->write-msa.in-msa read-sequence.out-sequence->sequences-to-msa.in-sequence } read-sequence.sequence->sequences-to-msa.in-sequence.sequence sequences-to-msa.msa->muscle.in-msa.msa muscle.msa->write-msa.in-msa.msa .iteration "Default iteration"{ id:13; write-msa { } read-sequence { } } .meta { visual { read-sequence { description:"

Read sequences

Reads sequence(s) from unset.

"; tooltip:"Reads sequences and annotations if any from local or remote files."; pos:"-705 -525"; style:ext; bg-color-ext:"0 128 128 64"; out-sequence.angle:360; } sequences-to-msa { description:"

Join sequences into alignment

Creates multiple sequence alignment from supplied sequences.

"; tooltip:"Creates multiple sequence alignment from sequences."; pos:"-540 -525"; style:ext; bg-color-ext:"0 128 128 64"; in-sequence.angle:180; out-msa.angle:360; } read-sequence.out-sequence->sequences-to-msa.in-sequence { text-pos:"-27.5 -24"; } muscle { description:"

Align with MUSCLE

Aligns each MSA supplied with MUSCLE using "MUSCLE default" mode.

"; tooltip:"MUSCLE is public domain multiple alignment software for protein and nucleotide sequences.

MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.

"; pos:"-330 -525"; style:ext; bg-color-ext:"0 128 128 64"; in-msa.angle:180; out-msa.angle:360; } sequences-to-msa.out-msa->muscle.in-msa { text-pos:"-43.5 -24"; } write-msa { description:"

Write alignment

Save all MSAs from Align with MUSCLE to unset.

"; tooltip:"Writes all supplied alignments to file(s) in selected format"; pos:"-150 -525"; style:ext; bg-color-ext:"0 128 128 64"; in-msa.angle:180; } muscle.out-msa->write-msa.in-msa { text-pos:"-45 -50"; } } } }