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.

-perm PERM

Specifies the guide tree permutation . PERM can be none , abc , acb and bca , default is none .

-stratified

Generate stratified ensemble .

-diversified

Generate diversified ensemble .

-replicates N

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.

-consiters 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.