align command
Align sequences using the PPP algorithm.
Examples
muscle -align seqs.fa -output aln.afa
muscle -align seqs.fa -output aln.afa -perturb 3 -perm abc
muscle -align seqs.fa -output stratified_ensemble.efa -stratified
muscle -align seqs.fa -output stratified_replicate.@.afa -stratified
muscle -align seqs.fa -output diversified_ensemble.efa -diversified
Description
The
align command uses the
PPP algorithm to
align sequences. Input must be in
FASTA format.
By default, a single alignment is generated using default parameters and output is in aligned FASTA
format.
If an
ensemble is generated and the output filename contains
@, each
replicate is written to a
different FASTA filename where
@ is replaced by the replicate name, e.g.
abc.3. Otherwise, all alignments
are written to one file in
ensemble FASTA (EFA) format.
Options
-perturb SEED
Integer random number seed for generating
HMM perturbations.
Default SEED=0, which uses default HMM parameters.
Number of
replicates,
default 4 for
-stratified and 100 for
-diversified.
With
-stratified, one replicate is generated for each
guide tree permutation, so the total number of replicates is 4×N.
Number of consistency iterations. Default 2.
-refineiters N
Number of refinement iterations. Default 100.
-nt
Input sequences use nucleotide alphabet (default auto-detect).
-amino
Input sequences use amino acid alphabet (default auto-detect).
-threads N
Number of threads. Default is the number of CPU cores, or 20
if the CPU has more than 20 cores.
