NAME

       muscle - Multiple alignment program of protein sequences

DESCRIPTION

       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.

USAGE

   Align FASTA input, write aligned FASTA (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

   Single replicate alignment:
              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.

   Calculate disperson of an ensemble:
              muscle -disperse ensemble.efa

   Extract replicate with highest total CC (diversified input recommended):
              muscle -maxcc ensemble.efa -output maxcc.afa

   Extract aligned FASTA files from EFA file:
              muscle -efa_explode ensemble.efa

   Convert FASTA to EFA, input has one filename per line:
              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.

   More documentation at:
              https://drive5.com/muscle

AUTHOR

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