muscle - Multiple alignment program of protein sequences

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

muscle 5.1                                        January 2022                                         MUSCLE(1)

       MUSCLE  is  a  multiple  alignment  program  for  protein  sequences. MUSCLE stands for multiple sequence
       comparison by log-expectation. In the authors tests, MUSCLE achieved the highest  scores  of  all  tested
       programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.

       muscle - Multiple alignment program of protein sequences

AlignFASTAinput,writealignedFASTA(AFA)output:
              muscle -align input.fa -output aln.afa

       Align  large  input  using Super5 algorithm if -align is too expensive, typically needed with more than a
       few hundred sequences:

              muscle -super5 input.fa -output aln.afa

   Singlereplicatealignment:
              muscle -align input.fa -perm PERM -perturb SEED -output aln.afa muscle -super5 input.fa -perm PERM
              -perturb SEED -output aln.afa

              PERM is guide tree permutation none, abc, acb, bca (default none).  SEED is perturbation  seed  0,
              1, 2... (default 0 = don't perturb).

       Ensemble  of  replicate  alignments, output in Ensemble FASTA (EFA) format, EFA has one aligned FASTA for
       each replicate with header line "<PERM.SEED":

              muscle  -align  input.fa  -stratified-output  stratified_ensemble.efa  muscle  -align   input.fa
              -diversified-output diversified_ensemble.afa

       -replicates N

              Number of replicates, defaults 4, 100, 100 for stratified,

              diversified,  resampled. With -stratified there is one replicate per guide tree permutation, total
              is 4 x N.

       Generate resampled ensemble from existing ensemble by sampling columns with replacement:

              muscle -resample ensemble.efa -output resampled.efa

       -maxgapfract F

              Maximum fraction of gaps in a column (F=0..1, default 0.5).

       -minconf CC

              Minimum column confidence (CC=0..1, default 0.5).

       If ensemble output filename has @, then one FASTA file  is  generated  for  each  replicate  where  @  is
       replaced by perm.s, otherwise all replicates are written to one EFA file.

   Calculatedispersonofanensemble:
              muscle -disperse ensemble.efa

   ExtractreplicatewithhighesttotalCC(diversifiedinputrecommended):
              muscle -maxcc ensemble.efa -output maxcc.afa

   ExtractalignedFASTAfilesfromEFAfile:
              muscle -efa_explode ensemble.efa

   ConvertFASTAtoEFA,inputhasonefilenameperline:
              muscle -fa2efa filenames.txt -output ensemble.efa

       Update  ensemble  by  adding two sequences of digits to each replicate, digits are column confidence (CC)
       values, e.g. "73" means CC=0.73, "++" is CC=1.0:

              muscle -addconfseqs ensemble.efa -output ensemble_cc.efa

       Calculate letter confidence (LC) values, -ref specifies the alignment to  compare  against  the  ensemble
       (e.g. from -maxcc), output is in aligned FASTA format with LC values 0, 1 ... 9 instead of letters:

              muscle -letterconf ensemble.efa -ref aln.afa -output letterconf.afa

       -html aln.html

              Alignment colored by LC in HTML format.

       -jalview aln.features

              Jalview feature file with LC values and colors.

   Moredocumentationat:
              https://drive5.com/muscle