super5 command

Align sequences using the Super5 algorithm .

Examples

muscle -super5 seqs.fa -output aln.afa
muscle -super5 seqs.fa -output aln.afa -perturb 3 -perm abc
muscle -super5 seqs.fa -output replicate.@.afa -perturb 3 -perm all
muscle -super5 seqs.fa -output replicates.efa -perturb 3 -perm all

Description

The super5 command uses the Super5 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. Super5 is generally used for aligning large sets of sequences where the PPP algorithm ( align command ) is too slow.

This command does not directly support generating complete ensembles, so the -stratified , -diversified and -replicates options are not supported. You can generate all guide tree permutations for a single HMM perturbation by using -perm all , this creates four alignments, one for each variant of the guide tree. If -perm all is set, and the output filename contains @ , then alignments are written to four different FASTA files where @ is replaced by is replaced by the replicate name, e.g. abc.3 . Otherwise, all four alignments are written to one file in ensemble FASTA (EFA) format.

To create a stratified ensemble , run super5 with -perm all once for each perturbation seed and combine the outputs. To create a diversified ensemble , run super5 once for each perturbation seed plus guide tree permutation and combine the outputs. Multiple FASTA files can be combined into a single EFA file by using the fa2efa command .

Options

-perturb SEED
-perm PERM
-consiters N
-refineiters N
-nt
-amino
-threads N